# Date 2008-01-16 Time 04:23:24 PST -0800 (1200486204.13 s)
#phil __OFF__

Command line arguments: "../294.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 29439
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 294

-------------------------------------------------------------------------------
  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: (69.1963, 46.6953, 87.6859, 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: 2.75, per 1000 atoms: 0.97


================================== 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: (69.1963, 46.6953, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8871 1.97077
Completeness in resolution range: 0.94862
Completeness with d_max=infinity: 0.945689

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8871
                             d_min =   1.9708

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: (69.1963, 46.6953, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8871 1.97077
Completeness in resolution range: 0.94862
Completeness with d_max=infinity: 0.945689

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8875 -  4.2168 [2176/2203]  1956   220  10.1%
  bin  2:  4.2168 -  3.3596 [2070/2086]  1864   206  10.0%
  bin  3:  3.3596 -  2.9386 [2062/2081]  1857   205   9.9%
  bin  4:  2.9386 -  2.6717 [2041/2071]  1835   206  10.1%
  bin  5:  2.6717 -  2.4811 [2009/2028]  1810   199   9.9%
  bin  6:  2.4811 -  2.3354 [2023/2048]  1818   205  10.1%
  bin  7:  2.3354 -  2.2188 [2014/2048]  1819   195   9.7%
  bin  8:  2.2188 -  2.1225 [1988/2018]  1781   207  10.4%
  bin  9:  2.1225 -  2.0410 [1979/2021]  1789   190   9.6%
  bin 10:  2.0410 -  1.9708 [1227/2046]  1101   126  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_294/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: 0.11 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:
        1.50 -     2.18: 13
        2.18 -     2.86: 1153
        2.86 -     3.54: 4450
        3.54 -     4.22: 9256
        4.22 -     4.90: 13568
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.497 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.667 3.040 -x+1,y+1/2,-z+1/2
  " NH1 ARG A  24 " - " O   GLY A  91 "  1.749 3.120 -x+1,y+1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.831 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28435 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_294/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_294/model_refine_001.geo

CPU time processing inputs: 7.73


============================ 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 = 69.19625 46.69535 87.68585 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: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3581   r_free= 0.3522   ksol= 0.00   Bsol= 0.00   scale= 0.960    |
|                                                                             |
| 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:   0.42 A                  |
| x-ray target function (ml) for work reflections: 6.111585                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8875 -  4.7030 0.99   1411  156 0.2868 0.2825      6.3741      6.3264|
|  2:  4.7030 -  3.7526 0.99   1354  152 0.2736 0.2899      6.4732      6.5224|
|  3:  3.7526 -  3.2841 0.99   1324  147 0.3190 0.2996      6.4302      6.4308|
|  4:  3.2841 -  2.9864 0.99   1329  142 0.3393 0.3690      6.3078      6.4066|
|  5:  2.9864 -  2.7739 0.99   1308  151 0.3648 0.3215      6.1571      6.0915|
|  6:  2.7739 -  2.6112 0.99   1309  142 0.3774 0.4240      6.0831      6.0809|
|  7:  2.6112 -  2.4811 0.99   1287  146 0.3738 0.3116      6.0569      5.9103|
|  8:  2.4811 -  2.3735 0.98   1287  145 0.4127 0.3793      6.0654      6.0359|
|  9:  2.3735 -  2.2825 0.98   1311  140 0.4167 0.4120      5.9932      6.0328|
| 10:  2.2825 -  2.2040 0.98   1295  143 0.4198 0.3750      6.0078      5.9074|
| 11:  2.2040 -  2.1353 0.99   1273  148 0.4235 0.4266      5.9203      5.9452|
| 12:  2.1353 -  2.0744 0.97   1274  136 0.4253 0.4063      5.8707      5.9199|
| 13:  2.0744 -  2.0199 0.98   1280  138 0.4352 0.4651      5.8025      5.7592|
| 14:  2.0199 -  1.9708 0.46    588   73 0.4058 0.3999      5.7723      5.6321|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8875 -  4.7030  1411   156  0.79  26.10   0.86     0.81      43630.86|
|  2:  4.7030 -  3.7526  1354   152  0.82  23.99   0.98     0.91      54567.40|
|  3:  3.7526 -  3.2841  1324   147  0.77  28.98   0.98     0.92      55298.23|
|  4:  3.2841 -  2.9864  1329   142  0.73  32.79   0.98     0.89      49312.74|
|  5:  2.9864 -  2.7739  1308   151  0.67  37.75   0.98     0.85      39701.76|
|  6:  2.7739 -  2.6112  1309   142  0.67  38.45   0.97     0.84      34375.43|
|  7:  2.6112 -  2.4811  1287   146  0.68  37.69   1.00     0.86      30764.85|
|  8:  2.4811 -  2.3735  1287   145  0.66  39.04   0.98     0.86      28280.58|
|  9:  2.3735 -  2.2825  1311   140  0.65  39.90   0.99     0.87      27442.90|
| 10:  2.2825 -  2.2040  1295   143  0.64  41.13   1.02     0.86      26345.24|
| 11:  2.2040 -  2.1353  1273   148  0.61  43.40   1.00     0.89      27227.72|
| 12:  2.1353 -  2.0744  1274   136  0.59  44.83   1.01     0.87      25870.74|
| 13:  2.0744 -  2.0199  1280   138  0.56  47.37   1.01     0.82      23572.16|
| 14:  2.0199 -  1.9708   588    73  0.57  46.90   1.05     0.71      19432.31|
|alpha:            min =        0.71 max =            0.92 mean =         0.86|
|beta:             min =    19432.31 max =        55298.23 mean =     35532.11|
|figures of merit: min =        0.00 max =            1.00 mean =         0.68|
|phase err.(work): min =        0.00 max =           90.00 mean =        37.20|
|phase err.(test): min =        0.00 max =           89.87 mean =        37.11|
|-----------------------------------------------------------------------------|

============================== 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 = 3.323288              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.260   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.719533              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.113   (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 |  1.497 -  1.837:        5 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.837 -  2.178:        8 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.178 -  2.518:       33 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.518 -  2.858:     1120 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.858 -  3.198:     1940 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.198 -  3.539:     2510 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.539 -  3.879:     4660 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.879 -  4.219:     4596 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.219 -  4.560:     6193 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.560 -  4.900:     7375 |
|-----------------------------------------------------------------------------|
|-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 |        0.173 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.112    4.900  1.497 |       0.346 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.766)------------------------------------------|
|    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: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3581   r_free= 0.3522   ksol= 0.00   Bsol= 0.00   scale= 0.960    |
|                                                                             |
| 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:   0.42 A                  |
| x-ray target function (ml) for work reflections: 6.111585                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3464   r_free= 0.3401   ksol= 0.32   Bsol= 37.20   scale= 0.979   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.08,-2.18,2.19,-0.00,0.00,0.00); trace/3= -0.35                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.42 A                  |
| x-ray target function (ml) for work reflections: 6.091623                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.853897              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.948   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.414639              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.843   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3464      final r-factor (work) = 0.2174          |
| start r-factor (free) = 0.3401      final r-factor (free) = 0.2449          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.8712 = 2.85 * 0.50 * 6.0955 + 1.00 * 0.1733                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.4042 = 2.85 * 0.50 * 5.8407 + 1.00 * 0.0699                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2174      final r-factor (work) = 0.2001          |
| start r-factor (free) = 0.2449      final r-factor (free) = 0.2520          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4280 = 0.41 * 1.00 * 5.8407 + 1.00 * 0.0062                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3688 = 0.41 * 1.00 * 5.6286 + 1.00 * 0.0349                               |
|-----------------------------------------------------------------------------|
| number of iterations = 6       |    number of function evaluations = 9      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.766)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    69.24   16.74    None  None   None       |
|    all(noH): 2823   0      0.00    69.24   16.74    None  None   None       |
|    Sol.    : 438    0      5.47    62.45   37.62    None  None   None       |
|    Mac.    : 2385   0      0.00    69.24   12.91    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 -   6.924:  408   |   5:    34.621 -  41.545:  119        |
|      1:     6.924 -  13.848: 1169   |   6:    41.545 -  48.469:   98        |
|      2:    13.848 -  20.772:  605   |   7:    48.469 -  55.393:   70        |
|      3:    20.772 -  27.697:  204   |   8:    55.393 -  62.317:   31        |
|      4:    27.697 -  34.621:  116   |   9:    62.317 -  69.241:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2001 r_free = 0.2520             target_work(ml) = 5.639         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1998 r_free = 0.2515             target_work(ml) = 5.639         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1998   r_free= 0.2515   ksol= 0.32   Bsol= 37.20   scale= 1.031   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.08,-2.18,2.19,-0.00,0.00,0.00); trace/3= -0.35                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.638784                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1978   r_free= 0.2499   ksol= 0.33   Bsol= 51.87   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.76,-2.64,-0.08,-0.00,-0.00,-0.00); trace/3= -1.83                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.635873                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.562643              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.344   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.283440              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.346   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1978      final r-factor (work) = 0.1382          |
| start r-factor (free) = 0.2499      final r-factor (free) = 0.1795          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.1155 = 3.56 * 0.50 * 5.6394 + 1.00 * 0.0699                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.8419 = 3.56 * 0.50 * 5.4928 + 1.00 * 0.0573                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1382      final r-factor (work) = 0.1283          |
| start r-factor (free) = 0.1795      final r-factor (free) = 0.1709          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6132 = 0.28 * 1.00 * 5.4928 + 1.00 * 0.0563                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5024 = 0.28 * 1.00 * 5.2717 + 1.00 * 0.0082                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.766)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    71.01   17.02    None  None   None       |
|    all(noH): 2823   0      0.00    71.01   17.02    None  None   None       |
|    Sol.    : 438    0      6.29    69.93   39.13    None  None   None       |
|    Mac.    : 2385   0      0.00    71.01   12.96    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 -   7.101:  350   |   5:    35.506 -  42.607:  101        |
|      1:     7.101 -  14.202: 1394   |   6:    42.607 -  49.708:   97        |
|      2:    14.202 -  21.304:  475   |   7:    49.708 -  56.810:   84        |
|      3:    21.304 -  28.405:  155   |   8:    56.810 -  63.911:   41        |
|      4:    28.405 -  35.506:  113   |   9:    63.911 -  71.012:   13        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1283 r_free = 0.1709             target_work(ml) = 5.247         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1281 r_free = 0.1709             target_work(ml) = 5.247         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1281   r_free= 0.1709   ksol= 0.33   Bsol= 51.87   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.76,-2.64,-0.08,-0.00,-0.00,-0.00); trace/3= -1.83                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.246630                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1282   r_free= 0.1709   ksol= 0.33   Bsol= 51.87   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.94,-2.47,-0.52,-0.00,-0.00,-0.00); trace/3= -1.98                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.245570                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.146343              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 121.742  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.348187              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 150.091  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1282      final r-factor (work) = 0.1161          |
| start r-factor (free) = 0.1709      final r-factor (free) = 0.1581          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7147 = 2.15 * 0.50 * 5.2716 + 1.00 * 0.0573                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6408 = 2.15 * 0.50 * 5.2044 + 1.00 * 0.0556                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1161      final r-factor (work) = 0.1143          |
| start r-factor (free) = 0.1581      final r-factor (free) = 0.1575          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8203 = 0.35 * 1.00 * 5.2044 + 1.00 * 0.0082                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8044 = 0.35 * 1.00 * 5.1584 + 1.00 * 0.0084                               |
|-----------------------------------------------------------------------------|
| number of iterations = 12      |    number of function evaluations = 13     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.766)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    73.81   16.89    None  None   None       |
|    all(noH): 2823   0      0.00    73.81   16.89    None  None   None       |
|    Sol.    : 438    0      0.00    71.30   39.06    None  None   None       |
|    Mac.    : 2385   0      0.82    73.81   12.81    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 -   7.381:  409   |   5:    36.903 -  44.283:  107        |
|      1:     7.381 -  14.761: 1433   |   6:    44.283 -  51.664:   98        |
|      2:    14.761 -  22.142:  413   |   7:    51.664 -  59.045:   72        |
|      3:    22.142 -  29.522:  144   |   8:    59.045 -  66.425:   35        |
|      4:    29.522 -  36.903:  103   |   9:    66.425 -  73.806:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1143 r_free = 0.1575             target_work(ml) = 5.156         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1143 r_free = 0.1575             target_work(ml) = 5.155         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1143   r_free= 0.1575   ksol= 0.33   Bsol= 51.87   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.94,-2.47,-0.52,-0.00,-0.00,-0.00); trace/3= -1.98                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.155488                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1142   r_free= 0.1574   ksol= 0.33   Bsol= 51.87   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.88,-2.34,-0.59,-0.00,-0.00,-0.00); trace/3= -1.94                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.155422                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.554659              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 148.557  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.109675              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 135.326  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1142      final r-factor (work) = 0.1092          |
| start r-factor (free) = 0.1574      final r-factor (free) = 0.1546          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6443 = 2.55 * 0.50 * 5.1582 + 1.00 * 0.0556                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6256 = 2.55 * 0.50 * 5.1355 + 1.00 * 0.0659                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1092      final r-factor (work) = 0.1106          |
| start r-factor (free) = 0.1546      final r-factor (free) = 0.1535          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.5715 = 0.11 * 1.00 * 5.1355 + 1.00 * 0.0083                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.5696 = 0.11 * 1.00 * 5.1354 + 1.00 * 0.0064                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 35     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.766)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.56    72.43   16.21    None  None   None       |
|    all(noH): 2823   0      1.56    72.43   16.21    None  None   None       |
|    Sol.    : 438    0      1.56    70.17   36.09    None  None   None       |
|    Mac.    : 2385   0      2.09    72.43   12.56    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:     1.563 -   8.650:  666   |   5:    36.997 -  44.083:  110        |
|      1:     8.650 -  15.736: 1289   |   6:    44.083 -  51.170:   86        |
|      2:    15.736 -  22.823:  351   |   7:    51.170 -  58.257:   42        |
|      3:    22.823 -  29.910:  130   |   8:    58.257 -  65.344:   18        |
|      4:    29.910 -  36.997:  125   |   9:    65.344 -  72.430:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1106 r_free = 0.1535             target_work(ml) = 5.131         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1104 r_free = 0.1534             target_work(ml) = 5.131         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1104   r_free= 0.1534   ksol= 0.33   Bsol= 51.87   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.88,-2.34,-0.59,-0.00,-0.00,-0.00); trace/3= -1.94                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.130764                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1104   r_free= 0.1534   ksol= 0.33   Bsol= 51.87   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.85,-2.28,-0.57,-0.00,-0.00,-0.00); trace/3= -1.90                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.130785                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.614513              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 160.847  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.707865              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 159.685  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1104      final r-factor (work) = 0.1123          |
| start r-factor (free) = 0.1534      final r-factor (free) = 0.1543          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.2111 = 1.61 * 0.50 * 5.1350 + 1.00 * 0.0659                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.2027 = 1.61 * 0.50 * 5.1392 + 1.00 * 0.0540                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1123      final r-factor (work) = 0.1104          |
| start r-factor (free) = 0.1543      final r-factor (free) = 0.1553          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6443 = 0.71 * 1.00 * 5.1392 + 1.00 * 0.0064                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6420 = 0.71 * 1.00 * 5.1327 + 1.00 * 0.0087                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.766)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.72    84.36   16.68    None  None   None       |
|    all(noH): 2823   0      0.72    84.36   16.68    None  None   None       |
|    Sol.    : 438    0      2.31    76.88   38.93    None  None   None       |
|    Mac.    : 2385   0      0.72    84.36   12.59    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:     0.725 -   9.088:  877   |   5:    42.542 -  50.905:   95        |
|      1:     9.088 -  17.452: 1207   |   6:    50.905 -  59.269:   78        |
|      2:    17.452 -  25.815:  265   |   7:    59.269 -  67.632:   42        |
|      3:    25.815 -  34.179:  125   |   8:    67.632 -  75.996:   10        |
|      4:    34.179 -  42.542:  120   |   9:    75.996 -  84.359:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1104 r_free = 0.1553             target_work(ml) = 5.137         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1104 r_free = 0.1554             target_work(ml) = 5.137         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1104   r_free= 0.1554   ksol= 0.33   Bsol= 51.87   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.85,-2.28,-0.57,-0.00,-0.00,-0.00); trace/3= -1.90                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.137477                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8875 -  4.7030 0.99   1411  156 0.1034 0.1317      5.4277      5.5729|
|  2:  4.7030 -  3.7526 0.99   1354  152 0.0869 0.1087      5.4501      5.6127|
|  3:  3.7526 -  3.2841 0.99   1324  147 0.1052 0.1539       5.464      5.8539|
|  4:  3.2841 -  2.9864 0.99   1329  142 0.1175 0.1531      5.4219      5.5819|
|  5:  2.9864 -  2.7739 0.99   1308  151 0.1277 0.1548      5.2948      5.4797|
|  6:  2.7739 -  2.6112 0.99   1309  142 0.1216 0.1973      5.1959      5.4894|
|  7:  2.6112 -  2.4811 0.99   1287  146 0.1252 0.1580      5.1661      5.3092|
|  8:  2.4811 -  2.3735 0.98   1287  145 0.1110 0.1640       5.051      5.2972|
|  9:  2.3735 -  2.2825 0.98   1311  140 0.1163 0.1905      5.0061      5.3522|
| 10:  2.2825 -  2.2040 0.98   1295  143 0.1095 0.1603      4.9312       5.127|
| 11:  2.2040 -  2.1353 0.99   1273  148 0.1109 0.1825      4.9163      5.2969|
| 12:  2.1353 -  2.0744 0.97   1274  136 0.1142 0.1535      4.8806      5.1346|
| 13:  2.0744 -  2.0199 0.98   1280  138 0.1048 0.1772       4.754      5.0152|
| 14:  2.0199 -  1.9708 0.46    588   73 0.0893 0.1674      4.6068      4.9139|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8875 -  4.7030  1411   156  0.94   9.61   0.98     0.95       7764.61|
|  2:  4.7030 -  3.7526  1354   152  0.95   7.98   1.01     1.00       9229.01|
|  3:  3.7526 -  3.2841  1324   147  0.93  11.23   1.02     1.02      10070.98|
|  4:  3.2841 -  2.9864  1329   142  0.92  13.05   1.01     0.99       9723.66|
|  5:  2.9864 -  2.7739  1308   151  0.91  15.26   0.99     0.97       7837.82|
|  6:  2.7739 -  2.6112  1309   142  0.90  16.31   0.98     0.95       6893.36|
|  7:  2.6112 -  2.4811  1287   146  0.91  15.34   0.98     0.95       6104.14|
|  8:  2.4811 -  2.3735  1287   145  0.91  14.76   0.99     0.97       5217.23|
|  9:  2.3735 -  2.2825  1311   140  0.91  15.20   0.99     0.95       4717.30|
| 10:  2.2825 -  2.2040  1295   143  0.90  15.41   0.99     0.96       4168.43|
| 11:  2.2040 -  2.1353  1273   148  0.90  16.12   0.99     0.95       4292.32|
| 12:  2.1353 -  2.0744  1274   136  0.91  15.51   1.00     0.99       3965.03|
| 13:  2.0744 -  2.0199  1280   138  0.90  15.97   0.99     0.96       3231.95|
| 14:  2.0199 -  1.9708   588    73  0.93  12.91   0.97     0.93       2312.91|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     2312.91 max =        10070.98 mean =      6304.57|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.99 mean =        13.89|
|phase err.(test): min =        0.00 max =           89.81 mean =        13.49|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1103   r_free= 0.1553   ksol= 0.32   Bsol= 51.85   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.63,-2.06,-0.38,-0.00,-0.00,-0.00); trace/3= -1.69                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.137481                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1103   r_free= 0.1553   ksol= 0.32   Bsol= 51.85   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.63,-2.06,-0.38,-0.00,-0.00,-0.00); trace/3= -1.69                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.137481                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8875 -  4.7030 0.99   1411  156 0.1033 0.1318      5.4271      5.5731|
|  2:  4.7030 -  3.7526 0.99   1354  152 0.0870 0.1087      5.4508       5.613|
|  3:  3.7526 -  3.2841 0.99   1324  147 0.1052 0.1539      5.4641      5.8539|
|  4:  3.2841 -  2.9864 0.99   1329  142 0.1174 0.1531      5.4218      5.5817|
|  5:  2.9864 -  2.7739 0.99   1308  151 0.1276 0.1547      5.2946      5.4792|
|  6:  2.7739 -  2.6112 0.99   1309  142 0.1216 0.1973      5.1958      5.4895|
|  7:  2.6112 -  2.4811 0.99   1287  146 0.1252 0.1580      5.1661      5.3092|
|  8:  2.4811 -  2.3735 0.98   1287  145 0.1110 0.1640      5.0511      5.2971|
|  9:  2.3735 -  2.2825 0.98   1311  140 0.1163 0.1906      5.0062      5.3522|
| 10:  2.2825 -  2.2040 0.98   1295  143 0.1095 0.1603      4.9313      5.1268|
| 11:  2.2040 -  2.1353 0.99   1273  148 0.1109 0.1825      4.9163      5.2967|
| 12:  2.1353 -  2.0744 0.97   1274  136 0.1142 0.1534      4.8805      5.1344|
| 13:  2.0744 -  2.0199 0.98   1280  138 0.1048 0.1773       4.754      5.0155|
| 14:  2.0199 -  1.9708 0.46    588   73 0.0893 0.1674      4.6072      4.9139|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8875 -  4.7030  1411   156  0.94   9.62   0.98     0.95       7754.88|
|  2:  4.7030 -  3.7526  1354   152  0.95   7.98   1.02     1.00       9229.44|
|  3:  3.7526 -  3.2841  1324   147  0.93  11.23   1.03     1.02      10073.34|
|  4:  3.2841 -  2.9864  1329   142  0.92  13.05   1.01     1.00       9720.29|
|  5:  2.9864 -  2.7739  1308   151  0.91  15.26   1.00     0.97       7836.33|
|  6:  2.7739 -  2.6112  1309   142  0.90  16.31   0.98     0.95       6891.26|
|  7:  2.6112 -  2.4811  1287   146  0.91  15.34   0.99     0.95       6103.44|
|  8:  2.4811 -  2.3735  1287   145  0.91  14.76   1.00     0.97       5217.40|
|  9:  2.3735 -  2.2825  1311   140  0.91  15.20   1.00     0.96       4717.40|
| 10:  2.2825 -  2.2040  1295   143  0.90  15.41   1.00     0.96       4167.53|
| 11:  2.2040 -  2.1353  1273   148  0.90  16.12   1.00     0.96       4290.27|
| 12:  2.1353 -  2.0744  1274   136  0.91  15.51   1.01     1.00       3964.29|
| 13:  2.0744 -  2.0199  1280   138  0.90  15.97   1.00     0.97       3232.22|
| 14:  2.0199 -  1.9708   588    73  0.93  12.91   0.98     0.94       2313.94|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2313.94 max =        10073.34 mean =      6303.23|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.98 mean =        13.89|
|phase err.(test): min =        0.00 max =           89.87 mean =        13.49|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.766)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.70    84.33   16.65    None  None   None       |
|    all(noH): 2823   0      0.70    84.33   16.65    None  None   None       |
|    Sol.    : 438    0      2.29    76.85   38.90    None  None   None       |
|    Mac.    : 2385   0      0.70    84.33   12.57    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:     0.701 -   9.064:  877   |   5:    42.518 -  50.881:   95        |
|      1:     9.064 -  17.428: 1207   |   6:    50.881 -  59.245:   78        |
|      2:    17.428 -  25.791:  265   |   7:    59.245 -  67.608:   42        |
|      3:    25.791 -  34.154:  125   |   8:    67.608 -  75.971:   10        |
|      4:    34.154 -  42.518:  120   |   9:    75.971 -  84.335:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 265         
Filter by distance & map next to the model:
   mapped sites are within: 0.503 - 5.457
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 259 from: 265
   mapped sites are within: 0.701 - 5.457

peak=    5.497 closest distance to " CB  ARG A 275 " =    0.930
peak=    5.418 closest distance to " NH2 ARG A  56 " =    2.173
peak=    5.321 closest distance to " CG  PRO A  54 " =    1.343
peak=    5.128 closest distance to " O   HOH Z 142 " =    1.737
peak=    5.103 closest distance to " CB  GLN A 223 " =    1.462
peak=    5.051 closest distance to " NE2 GLN A  11 " =    1.090
peak=    4.999 closest distance to " O   HOH Z 126 " =    1.892
peak=    4.768 closest distance to " CB  PRO A  54 " =    0.988
peak=    4.764 closest distance to " O   HOH Z 232 " =    2.439
peak=    4.638 closest distance to " O   HOH Z 287 " =    2.050
peak=    4.623 closest distance to " CG  PRO A 213 " =    1.253
peak=    4.604 closest distance to " O   HOH Z  78 " =    1.737
peak=    4.559 closest distance to " O   HOH Z 369 " =    2.306
peak=    4.534 closest distance to " CB  GLN A 183 " =    1.218
peak=    4.493 closest distance to " CG  PRO A  90 " =    1.259
peak=    4.493 closest distance to " CZ  PHE A 218 " =    1.071
peak=    4.451 closest distance to " CG  PRO A 198 " =    1.229
peak=    4.441 closest distance to " O   HOH Z 303 " =    2.104
peak=    4.438 closest distance to " CA  TYR A  30 " =    0.921
peak=    4.400 closest distance to " O   HOH Z 250 " =    1.520
peak=    4.394 closest distance to " CB  ARG A  79 " =    1.363
peak=    4.391 closest distance to " O   HOH Z 427 " =    2.963
peak=    4.365 closest distance to " CG2 VAL A 257 " =    0.860
peak=    4.365 closest distance to " O   HOH Z 402 " =    1.388
peak=    4.363 closest distance to " CG  PRO A 243 " =    1.049
peak=    4.334 closest distance to " O   HOH Z 298 " =    1.828
peak=    4.331 closest distance to " CB  GLU A 152 " =    1.201
peak=    4.312 closest distance to " ND2 ASN A 187 " =    1.475
peak=    4.292 closest distance to " CB  ARG A 190 " =    1.710
peak=    4.291 closest distance to " O   HOH Z 158 " =    3.055
peak=    4.290 closest distance to " CB  VAL A 265 " =    1.218
peak=    4.288 closest distance to " O   HOH Z 189 " =    2.783
peak=    4.272 closest distance to " O   HOH Z  15 " =    2.235
peak=    4.264 closest distance to " C   PRO A 198 " =    1.500
peak=    4.256 closest distance to " CD2 TRP A 179 " =    1.298
peak=    4.190 closest distance to " CB  SER A  63 " =    1.159
peak=    4.158 closest distance to " CB  ASN A 148 " =    1.454
peak=    4.139 closest distance to " O   HOH Z  78 " =    2.139
peak=    4.137 closest distance to " O  BHOH Z  74 " =    1.142
peak=    4.136 closest distance to " O   HOH Z 313 " =    2.035
peak=    4.128 closest distance to " O   HOH Z  40 " =    1.753
peak=    4.111 closest distance to " O   HOH Z 346 " =    1.722
peak=    4.104 closest distance to " O   SER A  87 " =    2.181
peak=    4.079 closest distance to " O   HOH Z  61 " =    1.681
peak=    4.062 closest distance to " CA  ASN A 215 " =    1.027
peak=    4.057 closest distance to " NZ  LYS A 117 " =    3.060
peak=    4.015 closest distance to " CB  GLU A  46 " =    1.004
peak=    3.985 closest distance to " N   TYR A 116 " =    1.557
peak=    3.971 closest distance to " O   HOH Z 272 " =    1.830
peak=    3.969 closest distance to " NZ  LYS A 119 " =    2.908
peak=    3.961 closest distance to " CE  LYS A  76 " =    0.871
peak=    3.943 closest distance to " O   HOH Z 209 " =    2.218
peak=    3.929 closest distance to " CB  VAL A 202 " =    1.583
peak=    3.926 closest distance to " CB  TRP A 266 " =    1.055
peak=    3.901 closest distance to " CB  ASN A 110 " =    1.082
peak=    3.884 closest distance to " O   ASN A  74 " =    1.373
peak=    3.881 closest distance to " O   HOH Z 265 " =    2.225
peak=    3.869 closest distance to " OG ASER A 258 " =    3.055
peak=    3.869 closest distance to " O   HOH Z  97 " =    2.417
peak=    3.868 closest distance to " O   HOH Z 234 " =    3.710
peak=    3.867 closest distance to " O   HOH Z 180 " =    2.201
peak=    3.867 closest distance to " O   HOH Z 128 " =    2.054
peak=    3.860 closest distance to " O   HOH Z 423 " =    1.922
peak=    3.853 closest distance to " O   HOH Z 392 " =    2.978
peak=    3.845 closest distance to " CG2 ILE A 120 " =    1.171
peak=    3.842 closest distance to " O   HOH Z 406 " =    1.603
peak=    3.841 closest distance to " CB  LEU A 228 " =    1.088
peak=    3.835 closest distance to " CA  ARG A  36 " =    1.007
peak=    3.833 closest distance to " ND2 ASN A 249 " =    0.897
peak=    3.829 closest distance to " CD  ARG A 159 " =    0.701
peak=    3.816 closest distance to " O   HOH Z 371 " =    1.701
peak=    3.803 closest distance to " CB  GLU A 277 " =    3.579
peak=    3.789 closest distance to " CB  ASN A  39 " =    0.884
peak=    3.757 closest distance to " O   HOH Z  44 " =    1.795
peak=    3.755 closest distance to " O   HOH Z 419 " =    2.302
peak=    3.721 closest distance to " O   HOH Z  92 " =    2.386
peak=    3.715 closest distance to " CB  THR A  31 " =    1.510
peak=    3.703 closest distance to " N   ASN A  39 " =    1.229
peak=    3.681 closest distance to " O   HOH Z 173 " =    1.907
peak=    3.681 closest distance to " O   HOH Z 353 " =    2.640
peak=    3.677 closest distance to " O   HOH Z 365 " =    2.775
peak=    3.659 closest distance to " O   HOH Z  43 " =    1.849
peak=    3.652 closest distance to " CB  GLU A 128 " =    0.967
peak=    3.648 closest distance to " O   HOH Z 327 " =    1.517
peak=    3.646 closest distance to " O   HOH Z 368 " =    3.606
peak=    3.635 closest distance to " O   HOH Z 291 " =    1.550
peak=    3.632 closest distance to " OG BSER A 164 " =    2.315
peak=    3.628 closest distance to " O  BHOH Z 338 " =    2.295
peak=    3.626 closest distance to " CB  SER A 212 " =    1.170
peak=    3.623 closest distance to " O   HOH Z  97 " =    2.024
peak=    3.622 closest distance to " O   HOH Z 389 " =    1.776
peak=    3.614 closest distance to " O   HOH Z 248 " =    1.523
peak=    3.610 closest distance to " O   HOH Z 359 " =    1.479
peak=    3.606 closest distance to " CB  ASN A 142 " =    1.047
peak=    3.593 closest distance to " NH1AARG A 145 " =    1.247
peak=    3.584 closest distance to " O   HOH Z 193 " =    1.804
peak=    3.576 closest distance to " CB  ALA A 114 " =    1.071
peak=    3.576 closest distance to " N   PHE A 130 " =    1.225
peak=    3.574 closest distance to " O   HOH Z  88 " =    2.831
peak=    3.574 closest distance to " CG  ARG A  66 " =    2.474
peak=    3.573 closest distance to " O   THR A 220 " =    1.254
peak=    3.565 closest distance to " O   HOH Z  59 " =    1.860
peak=    3.564 closest distance to " O   HOH Z   9 " =    2.080
peak=    3.551 closest distance to " CZ3 TRP A 266 " =    1.096
peak=    3.550 closest distance to " O   HOH Z  88 " =    2.566
peak=    3.546 closest distance to " CB  ASP A 140 " =    1.041
peak=    3.536 closest distance to " CA  SER A  87 " =    1.032
peak=    3.536 closest distance to " CG  GLU A  37 " =    0.868
peak=    3.532 closest distance to " O   HOH Z 185 " =    1.845
peak=    3.530 closest distance to " OD1 ASN A  69 " =    2.517
peak=    3.527 closest distance to " CA  ARG A 195 " =    1.199
peak=    3.519 closest distance to " CG1BVAL A  72 " =    1.646
peak=    3.514 closest distance to " O   HOH Z 214 " =    2.233
peak=    3.513 closest distance to " O   HOH Z 128 " =    2.140
peak=    3.512 closest distance to " O   HOH Z 203 " =    1.672
peak=    3.509 closest distance to " O   HOH Z  40 " =    1.408
peak=    3.506 closest distance to " CD  ARG A 269 " =    0.953
peak=    3.503 closest distance to " CA  THR A 264 " =    0.903
peak=    3.502 closest distance to " O   HOH Z 421 " =    1.945
peak=    3.496 closest distance to " CG1 ILE A  33 " =    1.210
peak=    3.488 closest distance to " CD2 LEU A 297 " =    0.913
peak=    3.478 closest distance to " O   HOH Z 261 " =    1.851
peak=    3.476 closest distance to " O   HOH Z 172 " =    3.418
peak=    3.474 closest distance to " CG AARG A 275 " =    1.085
peak=    3.472 closest distance to " O   HOH Z  10 " =    1.762
peak=    3.472 closest distance to " CG  LEU A 167 " =    1.269
peak=    3.471 closest distance to " O   HOH Z 371 " =    2.967
peak=    3.468 closest distance to " O   HOH Z 337 " =    3.573
peak=    3.468 closest distance to " CG  MET A 185 " =    1.104
peak=    3.467 closest distance to " O   HOH Z  66 " =    2.118
peak=    3.458 closest distance to " CB  PHE A 204 " =    0.714
peak=    3.457 closest distance to " O   HOH Z 417 " =    3.523
peak=    3.453 closest distance to " O   HOH Z 141 " =    1.661
peak=    3.451 closest distance to " O   HOH Z 403 " =    1.642
peak=    3.450 closest distance to " CB  GLN A  88 " =    1.183
peak=    3.446 closest distance to " O   HOH Z 233 " =    1.974
peak=    3.445 closest distance to " CB  ASP A 124 " =    0.752
peak=    3.441 closest distance to " CB  GLN A  89 " =    1.364
peak=    3.438 closest distance to " CG1 VAL A 153 " =    0.943
peak=    3.436 closest distance to " CB  SER A  26 " =    1.693
peak=    3.431 closest distance to " CE1 PHE A  38 " =    1.223
peak=    3.424 closest distance to " O   HOH Z  21 " =    1.784
peak=    3.420 closest distance to " CB  ILE A 120 " =    1.305
peak=    3.416 closest distance to " CB  ASN A 215 " =    1.147
peak=    3.409 closest distance to " CA  ASN A 217 " =    1.222
peak=    3.406 closest distance to " O   HOH Z 126 " =    1.533
peak=    3.406 closest distance to " O   HOH Z 132 " =    2.431
peak=    3.404 closest distance to " CG2AVAL A 121 " =    2.386
peak=    3.401 closest distance to " O   HOH Z   1 " =    2.014
peak=    3.399 closest distance to " O   HOH Z 411 " =    3.893
peak=    3.397 closest distance to " NE2 HIS A 207 " =    1.221
peak=    3.381 closest distance to " O   HOH Z 344 " =    3.183
peak=    3.379 closest distance to " CB  LEU A  83 " =    0.722
peak=    3.379 closest distance to " OG BSER A  99 " =    2.339
peak=    3.379 closest distance to " CB  SER A   3 " =    1.250
peak=    3.378 closest distance to " O   HOH Z 245 " =    1.318
peak=    3.375 closest distance to " CB  PRO A  90 " =    1.066
peak=    3.375 closest distance to " CB  ALA A 291 " =    1.193
peak=    3.372 closest distance to " O   HOH Z 280 " =    3.003
peak=    3.369 closest distance to " O   HOH Z 394 " =    3.911
peak=    3.361 closest distance to " CA  PHE A  59 " =    0.925
peak=    3.360 closest distance to " O   HOH Z 148 " =    3.493
peak=    3.356 closest distance to " O   HOH Z 285 " =    2.357
peak=    3.355 closest distance to " CD1 LEU A  96 " =    0.729
peak=    3.354 closest distance to " CD  LYS A 166 " =    1.210
peak=    3.354 closest distance to " O   HOH Z 234 " =    2.280
peak=    3.353 closest distance to " O   HOH Z 433 " =    1.847
peak=    3.352 closest distance to " O   HOH Z  61 " =    1.445
peak=    3.350 closest distance to " OG1 THR A 264 " =    0.751
peak=    3.348 closest distance to " CA  ALA A  84 " =    1.204
peak=    3.347 closest distance to " CG  GLN A  11 " =    1.876
peak=    3.345 closest distance to " CB  HIS A 108 " =    0.829
peak=    3.341 closest distance to " CB  TYR A 116 " =    0.747
peak=    3.340 closest distance to " NH2BARG A 145 " =    2.062
peak=    3.339 closest distance to " N   ARG A 156 " =    1.356
peak=    3.335 closest distance to " OD2 ASP A 286 " =    2.829
peak=    3.332 closest distance to " CB  ARG A 139 " =    1.053
peak=    3.327 closest distance to " O   HOH Z 273 " =    2.870
peak=    3.319 closest distance to " CA  MET A 105 " =    1.009
peak=    3.316 closest distance to " O   HOH Z 368 " =    2.098
peak=    3.316 closest distance to " NZ  LYS A  48 " =    1.151
peak=    3.315 closest distance to " CG  MET A 113 " =    1.017
peak=    3.313 closest distance to " CB  LYS A 117 " =    1.192
peak=    3.312 closest distance to " O   HOH Z 193 " =    1.942
peak=    3.309 closest distance to " O   HOH Z 213 " =    1.885
peak=    3.307 closest distance to " CA  ASN A 127 " =    1.138
peak=    3.307 closest distance to " CB  ALA A 242 " =    0.917
peak=    3.306 closest distance to " O   HOH Z 422 " =    2.575
peak=    3.301 closest distance to " O   HOH Z 329 " =    4.073
peak=    3.298 closest distance to " O   HOH Z 305 " =    3.496
peak=    3.295 closest distance to " O   HOH Z  78 " =    2.135
peak=    3.294 closest distance to " O   PHE A 192 " =    1.410
peak=    3.293 closest distance to " CB  LYS A 290 " =    0.989
peak=    3.293 closest distance to " CA  ALA A  51 " =    0.866
peak=    3.293 closest distance to " CA  ILE A 234 " =    0.967
peak=    3.292 closest distance to " O   HOH Z   1 " =    1.592
peak=    3.290 closest distance to " O   HOH Z 336 " =    1.679
peak=    3.289 closest distance to " CD1 ILE A 106 " =    0.803
peak=    3.289 closest distance to " CD1 ILE A 199 " =    1.102
peak=    3.286 closest distance to " N   ASP A 162 " =    1.082
peak=    3.284 closest distance to " CA  TYR A 116 " =    1.381
peak=    3.273 closest distance to " CG1 ILE A  49 " =    1.485
peak=    3.271 closest distance to " O   HOH Z 325 " =    2.466
peak=    3.266 closest distance to " O   HOH Z 298 " =    2.409
peak=    3.261 closest distance to " O   HOH Z 425 " =    1.922
peak=    3.260 closest distance to " CB  ALA A  34 " =    1.120
peak=    3.254 closest distance to " CA  ALA A 233 " =    1.202
peak=    3.250 closest distance to " O   HOH Z  44 " =    2.880
peak=    3.247 closest distance to " CB  PRO A 243 " =    1.295
peak=    3.246 closest distance to " CE1 TYR A 186 " =    1.302
peak=    3.241 closest distance to " O   HOH Z 251 " =    1.551
peak=    3.239 closest distance to " CA  VAL A 125 " =    1.080
peak=    3.239 closest distance to " O   ALA A   1 " =    1.675
peak=    3.233 closest distance to " CB  ALA A 248 " =    1.362
peak=    3.223 closest distance to " CA  ASP A 162 " =    1.043
peak=    3.223 closest distance to " CA  LYS A 290 " =    1.268
peak=    3.221 closest distance to " CA  LYS A 117 " =    1.210
peak=    3.219 closest distance to " CB  SER A 210 " =    0.764
peak=    3.218 closest distance to " O   HOH Z 227 " =    2.027
peak=    3.218 closest distance to " O   HOH Z 294 " =    1.473
peak=    3.205 closest distance to " CB  SER A 273 " =    0.865
peak=    3.195 closest distance to " CG2 ILE A  20 " =    1.414
peak=    3.191 closest distance to " CB  TRP A 179 " =    1.352
peak=    3.189 closest distance to " O   HOH Z 407 " =    2.447
peak=    3.184 closest distance to " O   HOH Z 147 " =    1.810
peak=    3.180 closest distance to " CG2 VAL A 197 " =    1.110
peak=    3.179 closest distance to " O   HOH Z 302 " =    2.045
peak=    3.179 closest distance to " CB  LEU A 300 " =    0.936
peak=    3.177 closest distance to " O   HOH Z 345 " =    3.278
peak=    3.175 closest distance to " O   HOH Z 245 " =    2.186
peak=    3.174 closest distance to " CB  ASP A 191 " =    1.246
peak=    3.174 closest distance to " O   HOH Z 342 " =    0.997
peak=    3.172 closest distance to " O   HOH Z 380 " =    1.980
peak=    3.171 closest distance to " O   HOH Z 257 " =    2.164
peak=    3.170 closest distance to " CA  ALA A 158 " =    1.335
peak=    3.169 closest distance to " CD1AILE A 234 " =    0.910
peak=    3.168 closest distance to " CZ2 TRP A 179 " =    1.811
peak=    3.165 closest distance to " CG1 ILE A 120 " =    1.111
peak=    3.158 closest distance to " CG  LYS A  76 " =    0.882
peak=    3.157 closest distance to " O   HOH Z 130 " =    2.169
peak=    3.152 closest distance to " CA  ALA A 291 " =    0.765
peak=    3.149 closest distance to " CB  SER A  62 " =    0.973
peak=    3.147 closest distance to " CA  ARG A 159 " =    1.262
peak=    3.144 closest distance to " OG  SER A  62 " =    2.760
peak=    3.140 closest distance to " ND1 HIS A  86 " =    1.779
peak=    3.137 closest distance to " O   HOH Z 299 " =    4.355
peak=    3.125 closest distance to " CE AMET A  47 " =    1.481
peak=    3.123 closest distance to " O   HOH Z 261 " =    1.880
peak=    3.112 closest distance to " O   HOH Z 430 " =    5.457
peak=    3.111 closest distance to " O   HOH Z 425 " =    1.258
peak=    3.104 closest distance to " O   HOH Z 383 " =    1.773
peak=    3.104 closest distance to " CA  SER A 146 " =    1.773
peak=    3.100 closest distance to " CA  ASP A 140 " =    1.147
peak=    3.058 closest distance to " O   HOH Z 409 " =    2.928
peak=    3.043 closest distance to " CB  ALA A 227 " =    1.101
peak=    3.036 closest distance to " CA  ALA A 299 " =    0.890
peak=    3.034 closest distance to " N   SER A 135 " =    1.245
peak=    3.026 closest distance to " CB  ALA A 114 " =    0.976
peak=    3.018 closest distance to " CA  GLU A  46 " =    1.046

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 191         
Filter by distance & map next to the model:
   mapped sites are within: 0.776 - 5.772
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 191 from: 191
   mapped sites are within: 0.776 - 5.772

peak=   -4.741 closest distance to " CG  GLN A  58 " =    1.035
peak=   -4.569 closest distance to " OG BSER A 134 " =    1.288
peak=   -4.472 closest distance to " CD  ARG A  14 " =    3.435
peak=   -4.438 closest distance to " C   HIS A 108 " =    1.112
peak=   -4.422 closest distance to " CG1 VAL A 112 " =    2.872
peak=   -4.385 closest distance to " CD  ARG A 156 " =    2.095
peak=   -4.303 closest distance to " CE  MET A 105 " =    2.453
peak=   -4.291 closest distance to " O   HOH Z 377 " =    2.100
peak=   -4.272 closest distance to " CD2 PHE A 192 " =    2.042
peak=   -4.266 closest distance to " CG  GLN A 223 " =    1.996
peak=   -4.241 closest distance to " O   HOH Z 266 " =    5.451
peak=   -4.229 closest distance to " O   PRO A 198 " =    1.247
peak=   -4.201 closest distance to " O   HOH Z 198 " =    1.474
peak=   -4.199 closest distance to " O   HOH Z 231 " =    2.256
peak=   -4.177 closest distance to " O   VAL A  67 " =    2.601
peak=   -4.124 closest distance to " CB  PRO A 243 " =    2.701
peak=   -4.062 closest distance to " CA  VAL A  67 " =    2.896
peak=   -4.012 closest distance to " O   HOH Z 372 " =    2.252
peak=   -3.952 closest distance to " CD1 LEU A 255 " =    2.797
peak=   -3.926 closest distance to " N   ALA A  43 " =    2.553
peak=   -3.887 closest distance to " CE2 TYR A  30 " =    2.757
peak=   -3.856 closest distance to " ND2 ASN A  45 " =    1.460
peak=   -3.841 closest distance to " CB  ASN A  39 " =    2.323
peak=   -3.837 closest distance to " OD2 ASP A 191 " =    1.394
peak=   -3.829 closest distance to " CB  ALA A  43 " =    2.532
peak=   -3.824 closest distance to " O   HOH Z 351 " =    1.448
peak=   -3.770 closest distance to " CZ3 TRP A 179 " =    1.199
peak=   -3.769 closest distance to " OD2 ASP A 171 " =    2.359
peak=   -3.754 closest distance to " OXT GLY A 302 " =    2.796
peak=   -3.723 closest distance to " ND2 ASN A 249 " =    2.226
peak=   -3.718 closest distance to " ND2 ASN A  45 " =    1.118
peak=   -3.713 closest distance to " CB  ALA A 161 " =    2.464
peak=   -3.703 closest distance to " CG2 ILE A 263 " =    2.259
peak=   -3.700 closest distance to " CD2 TYR A 293 " =    1.919
peak=   -3.696 closest distance to " O   HOH Z 407 " =    2.857
peak=   -3.686 closest distance to " OD1 ASP A 171 " =    1.593
peak=   -3.682 closest distance to " CZ  TYR A 169 " =    1.780
peak=   -3.674 closest distance to " O   HOH Z 185 " =    2.294
peak=   -3.672 closest distance to " CB  ALA A 248 " =    2.288
peak=   -3.661 closest distance to " CD  ARG A 139 " =    1.606
peak=   -3.640 closest distance to " N   ALA A 248 " =    1.594
peak=   -3.637 closest distance to " O   HOH Z 290 " =    1.248
peak=   -3.634 closest distance to " CG  ARG A 269 " =    2.250
peak=   -3.624 closest distance to " CG  PHE A 283 " =    2.707
peak=   -3.623 closest distance to " O   HOH Z 389 " =    1.949
peak=   -3.623 closest distance to " CE BMET A  47 " =    1.306
peak=   -3.622 closest distance to " CG  GLU A 277 " =    1.352
peak=   -3.622 closest distance to " O   HOH Z 357 " =    2.089
peak=   -3.621 closest distance to " O   SER A 210 " =    2.002
peak=   -3.620 closest distance to " O   HOH Z 102 " =    1.598
peak=   -3.620 closest distance to " NE2 GLN A 278 " =    1.726
peak=   -3.599 closest distance to " O   HOH Z  73 " =    2.458
peak=   -3.592 closest distance to " O   HOH Z 394 " =    1.458
peak=   -3.587 closest distance to " O   HOH Z 211 " =    1.521
peak=   -3.581 closest distance to " OD1 ASN A 148 " =    1.462
peak=   -3.567 closest distance to " CA  GLY A 203 " =    2.345
peak=   -3.566 closest distance to " O   HOH Z 196 " =    2.154
peak=   -3.562 closest distance to " O   HOH Z 313 " =    1.818
peak=   -3.561 closest distance to " O   HOH Z  63 " =    1.664
peak=   -3.557 closest distance to " OG  SER A  97 " =    2.223
peak=   -3.552 closest distance to " O   PHE A 218 " =    1.564
peak=   -3.550 closest distance to " NE  ARG A 156 " =    1.936
peak=   -3.540 closest distance to " O   ALA A  10 " =    1.684
peak=   -3.539 closest distance to " O   HOH Z  38 " =    1.721
peak=   -3.538 closest distance to " O   PRO A 163 " =    2.007
peak=   -3.536 closest distance to " CB  ALA A 291 " =    2.225
peak=   -3.535 closest distance to " CA  ASP A 298 " =    1.088
peak=   -3.524 closest distance to " CA  GLY A 241 " =    2.345
peak=   -3.518 closest distance to " CG2 THR A 178 " =    2.306
peak=   -3.516 closest distance to " CD1 ILE A 239 " =    2.409
peak=   -3.516 closest distance to " O   HOH Z 114 " =    3.074
peak=   -3.498 closest distance to " ND2 ASN A 187 " =    1.480
peak=   -3.480 closest distance to " CD1 PHE A  59 " =    2.050
peak=   -3.470 closest distance to " O   SER A  95 " =    1.537
peak=   -3.459 closest distance to " O   HOH Z  11 " =    1.723
peak=   -3.458 closest distance to " O   HOH Z  13 " =    1.742
peak=   -3.458 closest distance to " CD  GLU A 236 " =    1.059
peak=   -3.448 closest distance to " CG1 VAL A 112 " =    2.597
peak=   -3.442 closest distance to " O   HOH Z 165 " =    2.127
peak=   -3.440 closest distance to " O   HOH Z 139 " =    5.174
peak=   -3.438 closest distance to " O   VAL A 125 " =    2.253
peak=   -3.437 closest distance to " O   VAL A 189 " =    2.721
peak=   -3.436 closest distance to " CB  ASP A 132 " =    2.241
peak=   -3.435 closest distance to " O   HOH Z 348 " =    2.241
peak=   -3.435 closest distance to " O   HOH Z 353 " =    2.172
peak=   -3.435 closest distance to " CB  ALA A 291 " =    2.199
peak=   -3.429 closest distance to " O   HOH Z 174 " =    2.520
peak=   -3.424 closest distance to " NH2AARG A 275 " =    5.112
peak=   -3.415 closest distance to " CE2 PHE A 218 " =    2.451
peak=   -3.415 closest distance to " O   HOH Z 166 " =    1.948
peak=   -3.415 closest distance to " N   THR A  52 " =    1.743
peak=   -3.409 closest distance to " O   ALA A 292 " =    2.043
peak=   -3.402 closest distance to " CE2 PHE A  61 " =    2.603
peak=   -3.399 closest distance to " OE2 GLU A 152 " =    1.277
peak=   -3.388 closest distance to " O   ALA A 161 " =    1.651
peak=   -3.387 closest distance to " CD1 LEU A 101 " =    2.284
peak=   -3.387 closest distance to " O   HOH Z  15 " =    1.455
peak=   -3.379 closest distance to " CA  GLY A  57 " =    2.125
peak=   -3.376 closest distance to " O   HOH Z 429 " =    2.205
peak=   -3.370 closest distance to " CZ  PHE A  59 " =    1.501
peak=   -3.365 closest distance to " O   HOH Z 298 " =    2.433
peak=   -3.362 closest distance to " O   HOH Z 421 " =    3.166
peak=   -3.355 closest distance to " O   GLN A 240 " =    2.029
peak=   -3.348 closest distance to " N   THR A 157 " =    1.529
peak=   -3.347 closest distance to " ND2 ASN A  60 " =    4.113
peak=   -3.344 closest distance to " CZ  ARG A 259 " =    0.906
peak=   -3.342 closest distance to " N   MET A 188 " =    1.954
peak=   -3.342 closest distance to " O   HOH Z 243 " =    1.960
peak=   -3.337 closest distance to " O   HOH Z 134 " =    3.219
peak=   -3.334 closest distance to " CB  ASP A 286 " =    1.742
peak=   -3.331 closest distance to " NE2 GLN A 194 " =    1.875
peak=   -3.331 closest distance to " OD1 ASN A 187 " =    1.728
peak=   -3.325 closest distance to " O   TYR A 247 " =    2.834
peak=   -3.312 closest distance to " CB  ASP A 286 " =    2.095
peak=   -3.306 closest distance to " O   ARG A 145 " =    1.544
peak=   -3.306 closest distance to " CB  GLN A  11 " =    1.759
peak=   -3.298 closest distance to " O   HOH Z 298 " =    1.262
peak=   -3.289 closest distance to " CD1 LEU A   5 " =    2.407
peak=   -3.285 closest distance to " CG  TRP A 266 " =    2.008
peak=   -3.284 closest distance to " NH2 ARG A  66 " =    1.291
peak=   -3.284 closest distance to " O   HOH Z 317 " =    1.472
peak=   -3.282 closest distance to " O   VAL A 189 " =    1.666
peak=   -3.281 closest distance to " C   LEU A 143 " =    0.986
peak=   -3.271 closest distance to " N   GLN A  58 " =    1.693
peak=   -3.270 closest distance to " CB  TRP A  85 " =    2.559
peak=   -3.257 closest distance to " CG1 VAL A 250 " =    2.605
peak=   -3.255 closest distance to " CG  ASP A 231 " =    0.776
peak=   -3.255 closest distance to " CG1 VAL A 230 " =    2.009
peak=   -3.253 closest distance to " O   HOH Z 362 " =    5.771
peak=   -3.253 closest distance to " O   HOH Z 123 " =    2.385
peak=   -3.245 closest distance to " O   ASN A 252 " =    1.340
peak=   -3.242 closest distance to " O   HOH Z  37 " =    1.728
peak=   -3.241 closest distance to " OD2 ASP A  50 " =    1.573
peak=   -3.241 closest distance to " O   GLN A  89 " =    1.513
peak=   -3.235 closest distance to " O   MET A  40 " =    2.835
peak=   -3.235 closest distance to " CA  GLY A 241 " =    3.333
peak=   -3.228 closest distance to " O   HOH Z   6 " =    2.171
peak=   -3.224 closest distance to " CG  ARG A  66 " =    2.393
peak=   -3.222 closest distance to " CA  GLY A 133 " =    2.001
peak=   -3.222 closest distance to " O   TRP A  70 " =    1.434
peak=   -3.221 closest distance to " CE3 TRP A 274 " =    2.338
peak=   -3.219 closest distance to " C   ALA A 158 " =    1.481
peak=   -3.217 closest distance to " OD2 ASP A  50 " =    2.099
peak=   -3.217 closest distance to " O   HOH Z  71 " =    2.327
peak=   -3.211 closest distance to " CA  ASN A 127 " =    1.379
peak=   -3.210 closest distance to " O   LEU A 167 " =    1.444
peak=   -3.208 closest distance to " O   HOH Z  10 " =    1.455
peak=   -3.206 closest distance to " O   SER A 135 " =    1.450
peak=   -3.204 closest distance to " CD2 PHE A 225 " =    1.191
peak=   -3.204 closest distance to " OE1 GLN A  88 " =    1.070
peak=   -3.204 closest distance to " O   VAL A 174 " =    2.150
peak=   -3.203 closest distance to " O   HOH Z 369 " =    2.256
peak=   -3.195 closest distance to " O   HOH Z   6 " =    1.399
peak=   -3.188 closest distance to " CG  LEU A  83 " =    1.961
peak=   -3.185 closest distance to " NE2 GLN A  88 " =    1.195
peak=   -3.184 closest distance to " CB  ASP A 132 " =    2.387
peak=   -3.183 closest distance to " O   HOH Z 405 " =    2.735
peak=   -3.180 closest distance to " O   HOH Z  60 " =    2.131
peak=   -3.180 closest distance to " O   HOH Z 171 " =    2.006
peak=   -3.175 closest distance to " O   ALA A  34 " =    2.232
peak=   -3.173 closest distance to " O   HOH Z 281 " =    2.746
peak=   -3.161 closest distance to " CZ2 TRP A 274 " =    0.997
peak=   -3.155 closest distance to " NH2BARG A 275 " =    1.974
peak=   -3.154 closest distance to " CB  SER A 210 " =    1.128
peak=   -3.152 closest distance to " CG1 VAL A 197 " =    2.176
peak=   -3.151 closest distance to " O   HOH Z 191 " =    5.772
peak=   -3.151 closest distance to " O   HOH Z 253 " =    3.824
peak=   -3.148 closest distance to " O   SER A  22 " =    2.459
peak=   -3.146 closest distance to " O   ALA A 180 " =    1.222
peak=   -3.146 closest distance to " CG2BVAL A  41 " =    2.127
peak=   -3.135 closest distance to " O   GLY A  17 " =    1.039
peak=   -3.135 closest distance to " OG BSER A 134 " =    1.744
peak=   -3.132 closest distance to " O   HOH Z 371 " =    1.706
peak=   -3.131 closest distance to " CD2 PHE A  61 " =    2.296
peak=   -3.129 closest distance to " CE3 TRP A 150 " =    2.184
peak=   -3.127 closest distance to " ND2 ASN A  60 " =    1.318
peak=   -3.127 closest distance to " O   PRO A 198 " =    1.269
peak=   -3.126 closest distance to " NE2 GLN A  88 " =    1.825
peak=   -3.124 closest distance to " CB  TYR A  15 " =    2.185
peak=   -3.120 closest distance to " CG1 VAL A  78 " =    3.140
peak=   -3.117 closest distance to " O   ALA A  51 " =    1.224
peak=   -3.103 closest distance to " O   HOH Z 216 " =    1.489
peak=   -3.097 closest distance to " O   SER A 276 " =    1.705
peak=   -3.095 closest distance to " O   HOH Z 256 " =    1.432
peak=   -3.089 closest distance to " O   ALA A 180 " =    1.001
peak=   -3.086 closest distance to " CG1 VAL A 125 " =    1.821
peak=   -3.086 closest distance to " CG1AVAL A  41 " =    2.684
peak=   -3.080 closest distance to " O   LYS A  76 " =    1.882
peak=   -3.077 closest distance to " CZ  PHE A  38 " =    1.990
peak=   -3.076 closest distance to " CG  GLU A 152 " =    1.244
peak=   -3.064 closest distance to " CA  SER A 135 " =    1.322

================= 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    :  0.3581 0.3522   6.111585e+00   6.092417e+00
   1_bss:  0.3464 0.3401   6.091623e+00   6.067197e+00
   1_xyz:  0.2174 0.2449   5.685141e+00   5.773209e+00
   1_adp:  0.2001 0.2520   5.639410e+00   5.802215e+00
   1_occ:  0.1998 0.2515   5.638784e+00   5.801907e+00
   2_bss:  0.1978 0.2499   5.635873e+00   5.800375e+00
   2_xyz:  0.1382 0.1795   5.309512e+00   5.508288e+00
   2_adp:  0.1283 0.1709   5.247279e+00   5.459945e+00
   2_occ:  0.1281 0.1709   5.246630e+00   5.459744e+00
   3_bss:  0.1282 0.1709   5.245570e+00   5.457191e+00
   3_xyz:  0.1161 0.1581   5.166247e+00   5.392652e+00
   3_adp:  0.1143 0.1575   5.155804e+00   5.385488e+00
   3_occ:  0.1143 0.1575   5.155488e+00   5.385327e+00
   4_bss:  0.1142 0.1574   5.155422e+00   5.385277e+00
   4_xyz:  0.1092 0.1546   5.128069e+00   5.374733e+00
   4_adp:  0.1106 0.1535   5.131336e+00   5.367758e+00
   4_occ:  0.1104 0.1534   5.130764e+00   5.367595e+00
   5_bss:  0.1104 0.1534   5.130785e+00   5.367599e+00
   5_xyz:  0.1123 0.1543   5.143128e+00   5.375106e+00
   5_adp:  0.1104 0.1553   5.137357e+00   5.380686e+00
   5_occ:  0.1104 0.1554   5.137477e+00   5.380992e+00
   5_bss:  0.1103 0.1553   5.137481e+00   5.380945e+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  37.196  -1.080  -2.179   2.194  -0.000   0.000   0.000
   1_xyz:  0.321  37.196  -1.080  -2.179   2.194  -0.000   0.000   0.000
   1_adp:  0.321  37.196  -1.080  -2.179   2.194  -0.000   0.000   0.000
   1_occ:  0.321  37.196  -1.080  -2.179   2.194  -0.000   0.000   0.000
   2_bss:  0.328  51.870  -2.760  -2.641  -0.078  -0.000  -0.000  -0.000
   2_xyz:  0.328  51.870  -2.760  -2.641  -0.078  -0.000  -0.000  -0.000
   2_adp:  0.328  51.870  -2.760  -2.641  -0.078  -0.000  -0.000  -0.000
   2_occ:  0.328  51.870  -2.760  -2.641  -0.078  -0.000  -0.000  -0.000
   3_bss:  0.328  51.870  -2.937  -2.474  -0.523  -0.000  -0.000  -0.000
   3_xyz:  0.328  51.870  -2.937  -2.474  -0.523  -0.000  -0.000  -0.000
   3_adp:  0.328  51.870  -2.937  -2.474  -0.523  -0.000  -0.000  -0.000
   3_occ:  0.328  51.870  -2.937  -2.474  -0.523  -0.000  -0.000  -0.000
   4_bss:  0.326  51.870  -2.885  -2.342  -0.587  -0.000  -0.000  -0.000
   4_xyz:  0.326  51.870  -2.885  -2.342  -0.587  -0.000  -0.000  -0.000
   4_adp:  0.326  51.870  -2.885  -2.342  -0.587  -0.000  -0.000  -0.000
   4_occ:  0.326  51.870  -2.885  -2.342  -0.587  -0.000  -0.000  -0.000
   5_bss:  0.326  51.870  -2.854  -2.283  -0.570  -0.000  -0.000  -0.000
   5_xyz:  0.326  51.870  -2.854  -2.283  -0.570  -0.000  -0.000  -0.000
   5_adp:  0.326  51.870  -2.854  -2.283  -0.570  -0.000  -0.000  -0.000
   5_occ:  0.326  51.870  -2.854  -2.283  -0.570  -0.000  -0.000  -0.000
   5_bss:  0.322  51.846  -2.631  -2.059  -0.377  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  37.193 0.6786  0.8608    35528.140
   1_bss:  35.703 0.6943  0.8738    32045.561
   1_xyz:  23.494 0.8281  0.9946    14993.022
   1_adp:  24.392 0.8184  0.9853    15915.473
   1_occ:  24.396 0.8183  0.9853    15908.356
   2_bss:  24.206 0.8204  0.9370    15771.159
   2_xyz:  16.852 0.8904  0.9824     8185.887
   2_adp:  15.732 0.9003  0.9831     7501.634
   2_occ:  15.730 0.9004  0.9829     7493.453
   3_bss:  15.665 0.9009  0.9775     7435.804
   3_xyz:  14.222 0.9129  0.9809     6439.039
   3_adp:  14.053 0.9145  0.9745     6376.866
   3_occ:  14.051 0.9146  0.9744     6371.251
   4_bss:  14.050 0.9146  0.9758     6370.149
   4_xyz:  13.785 0.9167  0.9785     6232.172
   4_adp:  13.620 0.9181  0.9755     6187.765
   4_occ:  13.619 0.9181  0.9753     6179.204
   5_bss:  13.620 0.9181  0.9766     6179.456
   5_xyz:  13.721 0.9175  0.9750     6273.530
   5_adp:  13.841 0.9166  0.9680     6301.831
   5_occ:  13.845 0.9165  0.9679     6303.574
   5_bss:  13.847 0.9165  0.9745     6302.241
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.112   1.7326e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.112   1.7326e-01
   1_xyz:   1.108  0.008  0.072 15.085  0.005  4.110   6.9917e-02
   1_adp:   1.108  0.008  0.072 15.085  0.005  4.110   6.9917e-02
   1_occ:   1.108  0.008  0.072 15.085  0.005  4.110   6.9917e-02
   2_bss:   1.108  0.008  0.072 15.085  0.005  4.110   6.9917e-02
   2_xyz:   0.983  0.007  0.072 14.894  0.004  4.119   5.7326e-02
   2_adp:   0.983  0.007  0.072 14.894  0.004  4.119   5.7326e-02
   2_occ:   0.983  0.007  0.072 14.894  0.004  4.119   5.7326e-02
   3_bss:   0.983  0.007  0.072 14.894  0.004  4.119   5.7326e-02
   3_xyz:   0.962  0.007  0.072 14.723  0.004  4.110   5.5620e-02
   3_adp:   0.962  0.007  0.072 14.723  0.004  4.110   5.5620e-02
   3_occ:   0.962  0.007  0.072 14.723  0.004  4.110   5.5620e-02
   4_bss:   0.962  0.007  0.072 14.723  0.004  4.110   5.5620e-02
   4_xyz:   1.055  0.008  0.080 14.802  0.004  4.112   6.5858e-02
   4_adp:   1.055  0.008  0.080 14.802  0.004  4.112   6.5858e-02
   4_occ:   1.055  0.008  0.080 14.802  0.004  4.112   6.5858e-02
   5_bss:   1.055  0.008  0.080 14.802  0.004  4.112   6.5858e-02
   5_xyz:   0.943  0.006  0.073 14.518  0.004  4.112   5.4019e-02
   5_adp:   0.943  0.006  0.073 14.518  0.004  4.112   5.4019e-02
   5_occ:   0.943  0.006  0.073 14.518  0.004  4.112   5.4019e-02
   5_bss:   0.943  0.006  0.073 14.518  0.004  4.112   5.4019e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.497   2.4048e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.497   2.4048e-01
   1_xyz:   8.521  0.042  0.303 83.461  0.041  2.153   7.1360e-02
   1_adp:   8.521  0.042  0.303 83.461  0.041  2.153   7.1360e-02
   1_occ:   8.521  0.042  0.303 83.461  0.041  2.153   7.1360e-02
   2_bss:   8.521  0.042  0.303 83.461  0.041  2.153   7.1360e-02
   2_xyz:   6.761  0.042  0.253 83.143  0.040  2.295   4.2912e-02
   2_adp:   6.761  0.042  0.253 83.143  0.040  2.295   4.2912e-02
   2_occ:   6.761  0.042  0.253 83.143  0.040  2.295   4.2912e-02
   3_bss:   6.761  0.042  0.253 83.143  0.040  2.295   4.2912e-02
   3_xyz:   6.383  0.047  0.246 82.792  0.035  2.340   3.8440e-02
   3_adp:   6.383  0.047  0.246 82.792  0.035  2.340   3.8440e-02
   3_occ:   6.383  0.047  0.246 82.792  0.035  2.340   3.8440e-02
   4_bss:   6.383  0.047  0.246 82.792  0.035  2.340   3.8440e-02
   4_xyz:   6.895  0.052  0.273 83.367  0.037  2.299   4.8672e-02
   4_adp:   6.895  0.052  0.273 83.367  0.037  2.299   4.8672e-02
   4_occ:   6.895  0.052  0.273 83.367  0.037  2.299   4.8672e-02
   5_bss:   6.895  0.052  0.273 83.367  0.037  2.299   4.8672e-02
   5_xyz:   6.336  0.046  0.236 83.198  0.037  2.355   3.3936e-02
   5_adp:   6.336  0.046  0.236 83.198  0.037  2.355   3.3936e-02
   5_occ:   6.336  0.046  0.236 83.198  0.037  2.355   3.3936e-02
   5_bss:   6.336  0.046  0.236 83.198  0.037  2.355   3.3936e-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:  69.24   0.00  16.74  69.24   0.00  12.91  62.45   5.47  37.62
   1_occ:  69.24   0.00  16.74  69.24   0.00  12.91  62.45   5.47  37.62
   2_bss:  69.24   0.00  16.74  69.24   0.00  12.91  62.45   5.47  37.62
   2_xyz:  69.24   0.00  16.74  69.24   0.00  12.91  62.45   5.47  37.62
   2_adp:  71.01   0.00  17.02  71.01   0.00  12.96  69.93   6.29  39.13
   2_occ:  71.01   0.00  17.02  71.01   0.00  12.96  69.93   6.29  39.13
   3_bss:  71.01   0.00  17.02  71.01   0.00  12.96  69.93   6.29  39.13
   3_xyz:  71.01   0.00  17.02  71.01   0.00  12.96  69.93   6.29  39.13
   3_adp:  73.81   0.00  16.89  73.81   0.82  12.81  71.30   0.00  39.06
   3_occ:  73.81   0.00  16.89  73.81   0.82  12.81  71.30   0.00  39.06
   4_bss:  73.81   0.00  16.89  73.81   0.82  12.81  71.30   0.00  39.06
   4_xyz:  73.81   0.00  16.89  73.81   0.82  12.81  71.30   0.00  39.06
   4_adp:  72.43   1.56  16.21  72.43   2.09  12.56  70.17   1.56  36.09
   4_occ:  72.43   1.56  16.21  72.43   2.09  12.56  70.17   1.56  36.09
   5_bss:  72.43   1.56  16.21  72.43   2.09  12.56  70.17   1.56  36.09
   5_xyz:  72.43   1.56  16.21  72.43   2.09  12.56  70.17   1.56  36.09
   5_adp:  84.36   0.72  16.68  84.36   0.72  12.59  76.88   2.31  38.93
   5_occ:  84.36   0.72  16.68  84.36   0.72  12.59  76.88   2.31  38.93
   5_bss:  84.33   0.70  16.65  84.33   0.70  12.57  76.85   2.29  38.90
------------------------------------------------------------------------
 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:    1.635    0.012    0.273
   1_adp:    1.635    0.012    0.273
   1_occ:    1.635    0.012    0.273
   2_bss:    1.635    0.012    0.273
   2_xyz:    1.050    0.036    0.391
   2_adp:    1.050    0.036    0.391
   2_occ:    1.050    0.036    0.391
   3_bss:    1.050    0.036    0.391
   3_xyz:    0.988    0.059    0.424
   3_adp:    0.988    0.059    0.424
   3_occ:    0.988    0.059    0.424
   4_bss:    0.988    0.059    0.424
   4_xyz:    1.229    0.054    0.443
   4_adp:    1.229    0.054    0.443
   4_occ:    1.229    0.054    0.443
   5_bss:    1.229    0.054    0.443
   5_xyz:    1.356    0.050    0.446
   5_adp:    1.356    0.050    0.446
   5_occ:    1.356    0.050    0.446
   5_bss:    1.356    0.050    0.446
------------------------------------------------------------------------

CPU time actual refinement: 268.02


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_294/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_294/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_294/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_294/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_294/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 267.89 
  Macro-tasks:
    bulk solvent and scale       = 30.59  
    individual site refinement   = 109.32 
    weights calculation          = 24.69  
    collect and process          = 5.48   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 170.19 
  Micro-tasks:
    mask                            = 1.01   
    f_calc                          = 85.30  
    alpha_beta                      = 6.52   
    target                          = 0.93   
    gradients_wrt_atomic_parameters = 92.44  
    fmodel                         = 5.36   
    r_factors                      = 0.18   
    phase_errors                   = 9.18   
    foms                           = 0.27   
    TOTAL for micro-tasks          = 201.19 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 3.853 micro seconds
Total CPU time: 4.65 minutes
from_scatterers_fft:    627 calls, 84.92 s
gradients_fft:          572 calls, 81.24 s

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

# Date 2008-01-16 Time 04:28:02 PST -0800 (1200486482.41 s)
Start R-work = 0.3581, R-free = 0.3522 (no bulk solvent and anisotropic scale)
Final R-work = 0.1341, R-free = 0.1742 (no bulk solvent and anisotropic scale)

Start R-work = 0.3464, R-free = 0.3401
Final R-work = 0.1103, R-free = 0.1553