# Date 2008-01-16 Time 04:40:48 PST -0800 (1200487248.35 s)
#phil __OFF__

Command line arguments: "../416.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 26113
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 416

-------------------------------------------------------------------------------
  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: (69.5475, 46.6953, 88.1178, 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: 3.29, per 1000 atoms: 1.17


================================== 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: (69.5475, 46.6953, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.962 1.98076
Completeness in resolution range: 0.953004
Completeness with d_max=infinity: 0.950046

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9620
                             d_min =   1.9808

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: (69.5475, 46.6953, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.962 1.98076
Completeness in resolution range: 0.953004
Completeness with d_max=infinity: 0.950046

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9625 -  4.2381 [2165/2189]  1946   219  10.1%
  bin  2:  4.2381 -  3.3766 [2061/2080]  1856   205   9.9%
  bin  3:  3.3766 -  2.9535 [2049/2068]  1848   201   9.8%
  bin  4:  2.9535 -  2.6852 [2031/2061]  1820   211  10.4%
  bin  5:  2.6852 -  2.4937 [2005/2024]  1808   197   9.8%
  bin  6:  2.4937 -  2.3472 [2013/2038]  1810   203  10.1%
  bin  7:  2.3472 -  2.2301 [2010/2038]  1813   197   9.8%
  bin  8:  2.2301 -  2.1333 [1975/2011]  1772   203  10.3%
  bin  9:  2.1333 -  2.0514 [1981/2023]  1788   193   9.7%
  bin 10:  2.0514 -  1.9808 [1299/2023]  1169   130  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_416/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: 0.13 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:
        1.40 -     2.10: 11
        2.10 -     2.80: 736
        2.80 -     3.50: 4439
        3.50 -     4.20: 9312
        4.20 -     4.90: 13768
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.399 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.655 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.751 3.040 -x+1,y+1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.840 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28261 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_416/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_416/model_refine_001.geo

CPU time processing inputs: 9.24


============================ 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 = 69.5475 46.69535 88.1178 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: 1.98 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3669   r_free= 0.3626   ksol= 0.00   Bsol= 0.00   scale= 0.949    |
|                                                                             |
| 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:   0.45 A                  |
| x-ray target function (ml) for work reflections: 6.136129                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9625 -  4.7269 0.99   1405  155 0.2960 0.2886      6.4048      6.3234|
|  2:  4.7269 -  3.7716 0.99   1352  151 0.2829 0.3174      6.5202      6.6005|
|  3:  3.7716 -  3.3007 0.99   1310  149 0.3308 0.2995      6.4838      6.4356|
|  4:  3.3007 -  3.0016 0.99   1326  139 0.3498 0.3844      6.3471      6.4154|
|  5:  3.0016 -  2.7879 0.99   1296  149 0.3804 0.3247      6.1986      6.1356|
|  6:  2.7879 -  2.6245 0.99   1305  143 0.3807 0.4308      6.1023      6.0814|
|  7:  2.6245 -  2.4937 0.99   1284  147 0.3816 0.3394      6.0771      5.9883|
|  8:  2.4937 -  2.3856 0.98   1290  142 0.4220 0.3884      6.0973      6.0526|
|  9:  2.3856 -  2.2941 0.98   1285  139 0.4143 0.4159      6.0022      6.0499|
| 10:  2.2941 -  2.2152 0.99   1291  144 0.4346 0.4092      6.0245      5.9451|
| 11:  2.2152 -  2.1461 0.98   1274  143 0.4341 0.4107      5.9515      5.9368|
| 12:  2.1461 -  2.0849 0.97   1262  139 0.4381 0.3938      5.8851      5.9338|
| 13:  2.0849 -  2.0302 0.99   1271  138 0.4317 0.4839      5.8059      5.7796|
| 14:  2.0302 -  1.9808 0.52    679   81 0.4013 0.3903      5.7605      5.6559|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9625 -  4.7269  1405   155  0.80  25.26   0.85     0.82      41588.93|
|  2:  4.7269 -  3.7716  1352   151  0.82  24.67   0.96     0.90      57463.41|
|  3:  3.7716 -  3.3007  1310   149  0.76  29.96   0.96     0.91      59702.68|
|  4:  3.3007 -  3.0016  1326   139  0.71  34.31   0.96     0.87      53095.82|
|  5:  3.0016 -  2.7879  1296   149  0.66  39.06   0.97     0.83      42069.79|
|  6:  2.7879 -  2.6245  1305   143  0.64  40.31   0.97     0.82      37044.35|
|  7:  2.6245 -  2.4937  1284   147  0.65  39.74   0.98     0.83      33336.86|
|  8:  2.4937 -  2.3856  1290   142  0.64  40.74   0.96     0.82      30623.31|
|  9:  2.3856 -  2.2941  1285   139  0.63  41.45   0.99     0.83      29300.64|
| 10:  2.2941 -  2.2152  1291   144  0.61  43.53   1.00     0.82      28197.52|
| 11:  2.2152 -  2.1461  1274   143  0.59  45.18   0.99     0.85      29212.13|
| 12:  2.1461 -  2.0849  1262   139  0.58  46.31   1.00     0.84      27355.44|
| 13:  2.0849 -  2.0302  1271   138  0.55  47.98   1.00     0.80      24327.79|
| 14:  2.0302 -  1.9808   679    81  0.58  46.27   1.04     0.73      19150.26|
|alpha:            min =        0.73 max =            0.91 mean =         0.84|
|beta:             min =    19150.26 max =        59702.68 mean =     37415.16|
|figures of merit: min =        0.00 max =            1.00 mean =         0.66|
|phase err.(work): min =        0.00 max =           89.99 mean =        38.47|
|phase err.(test): min =        0.00 max =           89.67 mean =        38.41|
|-----------------------------------------------------------------------------|

============================== 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 = 6.558540              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.204   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.784137              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.178   (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 |  1.399 -  1.749:        2 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.749 -  2.099:        9 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.099 -  2.449:       20 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.449 -  2.799:      716 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.799 -  3.150:     2060 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.150 -  3.500:     2379 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.500 -  3.850:     4567 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.850 -  4.200:     4745 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.200 -  4.550:     6239 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.550 -  4.900:     7529 |
|-----------------------------------------------------------------------------|
|-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 |        0.172 |
| 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  1.399 |       0.322 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.879)------------------------------------------|
|    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: 1.98 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3669   r_free= 0.3626   ksol= 0.00   Bsol= 0.00   scale= 0.949    |
|                                                                             |
| 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:   0.45 A                  |
| x-ray target function (ml) for work reflections: 6.136129                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3523   r_free= 0.3484   ksol= 0.32   Bsol= 39.20   scale= 0.974   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.29,-2.31,4.30,-0.00,0.00,0.00); trace/3= -0.10                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.44 A                  |
| x-ray target function (ml) for work reflections: 6.113980                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.558498              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.009   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.447547              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.918   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3523      final r-factor (work) = 0.2020          |
| start r-factor (free) = 0.3484      final r-factor (free) = 0.2299          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.1630 = 5.56 * 0.50 * 6.1133 + 1.00 * 0.1725                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.2939 = 5.56 * 0.50 * 5.8327 + 1.00 * 0.0834                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2020      final r-factor (work) = 0.1860          |
| start r-factor (free) = 0.2299      final r-factor (free) = 0.2379          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6169 = 0.45 * 1.00 * 5.8327 + 1.00 * 0.0065                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5425 = 0.45 * 1.00 * 5.5580 + 1.00 * 0.0550                               |
|-----------------------------------------------------------------------------|
| number of iterations = 6       |    number of function evaluations = 6      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.879)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    81.19   16.79    None  None   None       |
|    all(noH): 2823   0      0.00    81.19   16.79    None  None   None       |
|    Sol.    : 438    0      4.54    62.78   38.08    None  None   None       |
|    Mac.    : 2385   0      0.00    81.19   12.88    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 -   8.119:  577   |   5:    40.593 -  48.712:  121        |
|      1:     8.119 -  16.237: 1280   |   6:    48.712 -  56.831:   81        |
|      2:    16.237 -  24.356:  458   |   7:    56.831 -  64.949:   23        |
|      3:    24.356 -  32.475:  153   |   8:    64.949 -  73.068:    0        |
|      4:    32.475 -  40.593:  129   |   9:    73.068 -  81.187:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1860 r_free = 0.2379             target_work(ml) = 5.574         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1858 r_free = 0.2373             target_work(ml) = 5.573         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1858   r_free= 0.2373   ksol= 0.32   Bsol= 39.20   scale= 1.037   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.29,-2.31,4.30,-0.00,0.00,0.00); trace/3= -0.10                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.572937                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1820   r_free= 0.2351   ksol= 0.33   Bsol= 55.88   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.11,-2.68,0.55,-0.00,0.00,0.00); trace/3= -1.75                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.563163                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.156421              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.821  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.363857              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.206   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1820      final r-factor (work) = 0.1411          |
| start r-factor (free) = 0.2351      final r-factor (free) = 0.1827          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0875 = 2.16 * 0.50 * 5.5686 + 1.00 * 0.0834                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9405 = 2.16 * 0.50 * 5.4601 + 1.00 * 0.0533                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1411      final r-factor (work) = 0.1325          |
| start r-factor (free) = 0.1827      final r-factor (free) = 0.1775          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0980 = 0.36 * 1.00 * 5.4601 + 1.00 * 0.1113                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9370 = 0.36 * 1.00 * 5.2981 + 1.00 * 0.0092                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.879)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    73.43   17.22    None  None   None       |
|    all(noH): 2823   0      0.00    73.43   17.22    None  None   None       |
|    Sol.    : 438    0      5.73    73.27   40.32    None  None   None       |
|    Mac.    : 2385   0      0.00    73.43   12.97    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 -   7.343:  433   |   5:    36.714 -  44.057:   97        |
|      1:     7.343 -  14.686: 1359   |   6:    44.057 -  51.399:   97        |
|      2:    14.686 -  22.028:  447   |   7:    51.399 -  58.742:   77        |
|      3:    22.028 -  29.371:  145   |   8:    58.742 -  66.085:   43        |
|      4:    29.371 -  36.714:  108   |   9:    66.085 -  73.428:   17        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1325 r_free = 0.1775             target_work(ml) = 5.279         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1324 r_free = 0.1775             target_work(ml) = 5.278         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1324   r_free= 0.1775   ksol= 0.33   Bsol= 55.88   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.11,-2.68,0.55,-0.00,0.00,0.00); trace/3= -1.75                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.278350                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1322   r_free= 0.1770   ksol= 0.33   Bsol= 59.67   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.92,-2.38,-0.07,-0.00,-0.00,-0.00); trace/3= -1.79                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.276037                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.221426              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 118.490  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.611931              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 140.652  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1322      final r-factor (work) = 0.1179          |
| start r-factor (free) = 0.1770      final r-factor (free) = 0.1622          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9370 = 2.22 * 0.50 * 5.2973 + 1.00 * 0.0533                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8634 = 2.22 * 0.50 * 5.2260 + 1.00 * 0.0587                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1179      final r-factor (work) = 0.1155          |
| start r-factor (free) = 0.1622      final r-factor (free) = 0.1596          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2071 = 0.61 * 1.00 * 5.2260 + 1.00 * 0.0092                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1748 = 0.61 * 1.00 * 5.1724 + 1.00 * 0.0097                               |
|-----------------------------------------------------------------------------|
| number of iterations = 21      |    number of function evaluations = 22     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.879)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.66    82.31   17.18    None  None   None       |
|    all(noH): 2823   0      0.66    82.31   17.18    None  None   None       |
|    Sol.    : 438    0      2.01    81.20   40.76    None  None   None       |
|    Mac.    : 2385   0      0.66    82.31   12.85    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.663 -   8.827:  775   |   5:    41.485 -  49.649:   98        |
|      1:     8.827 -  16.992: 1238   |   6:    49.649 -  57.813:   88        |
|      2:    16.992 -  25.156:  307   |   7:    57.813 -  65.978:   52        |
|      3:    25.156 -  33.320:  130   |   8:    65.978 -  74.142:   22        |
|      4:    33.320 -  41.485:  104   |   9:    74.142 -  82.306:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1155 r_free = 0.1596             target_work(ml) = 5.165         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1154 r_free = 0.1596             target_work(ml) = 5.165         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1154   r_free= 0.1596   ksol= 0.33   Bsol= 59.67   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.92,-2.38,-0.07,-0.00,-0.00,-0.00); trace/3= -1.79                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.164989                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1153   r_free= 0.1595   ksol= 0.33   Bsol= 59.67   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.70,-2.21,-0.22,-0.00,-0.00,-0.00); trace/3= -1.71                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.164770                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.864011              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 137.721  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.120291              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 128.303  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1153      final r-factor (work) = 0.1099          |
| start r-factor (free) = 0.1595      final r-factor (free) = 0.1569          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.4655 = 2.86 * 0.50 * 5.1723 + 1.00 * 0.0587                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.4359 = 2.86 * 0.50 * 5.1441 + 1.00 * 0.0695                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1099      final r-factor (work) = 0.1114          |
| start r-factor (free) = 0.1569      final r-factor (free) = 0.1552          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6284 = 0.12 * 1.00 * 5.1441 + 1.00 * 0.0096                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6259 = 0.12 * 1.00 * 5.1453 + 1.00 * 0.0070                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 33     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.879)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.78    77.13   16.29    None  None   None       |
|    all(noH): 2823   0      1.78    77.13   16.29    None  None   None       |
|    Sol.    : 438    0      3.08    74.72   36.91    None  None   None       |
|    Mac.    : 2385   0      1.78    77.13   12.50    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:     1.784 -   9.318:  901   |   5:    39.458 -  46.993:   90        |
|      1:     9.318 -  16.853: 1145   |   6:    46.993 -  54.528:   81        |
|      2:    16.853 -  24.388:  292   |   7:    54.528 -  62.062:   32        |
|      3:    24.388 -  31.923:  130   |   8:    62.062 -  69.597:   16        |
|      4:    31.923 -  39.458:  128   |   9:    69.597 -  77.132:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1114 r_free = 0.1552             target_work(ml) = 5.139         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1113 r_free = 0.1552             target_work(ml) = 5.139         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1113   r_free= 0.1552   ksol= 0.33   Bsol= 59.67   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.70,-2.21,-0.22,-0.00,-0.00,-0.00); trace/3= -1.71                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.139007                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1113   r_free= 0.1553   ksol= 0.32   Bsol= 50.66   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.64,-2.15,-0.24,-0.00,-0.00,-0.00); trace/3= -1.68                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.139325                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.581710              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 158.401  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.554611              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 158.972  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1113      final r-factor (work) = 0.1105          |
| start r-factor (free) = 0.1553      final r-factor (free) = 0.1561          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7107 = 2.58 * 0.50 * 5.1449 + 1.00 * 0.0695                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6967 = 2.58 * 0.50 * 5.1364 + 1.00 * 0.0664                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1105      final r-factor (work) = 0.1092          |
| start r-factor (free) = 0.1561      final r-factor (free) = 0.1563          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8556 = 0.55 * 1.00 * 5.1364 + 1.00 * 0.0069                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8542 = 0.55 * 1.00 * 5.1308 + 1.00 * 0.0086                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.879)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.95    81.53   16.49    None  None   None       |
|    all(noH): 2823   0      0.95    81.53   16.49    None  None   None       |
|    Sol.    : 438    0      4.00    79.13   38.52    None  None   None       |
|    Mac.    : 2385   0      0.95    81.53   12.45    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:     0.945 -   9.004:  884   |   5:    41.240 -  49.299:   94        |
|      1:     9.004 -  17.063: 1175   |   6:    49.299 -  57.358:   86        |
|      2:    17.063 -  25.122:  274   |   7:    57.358 -  65.417:   38        |
|      3:    25.122 -  33.181:  133   |   8:    65.417 -  73.476:   13        |
|      4:    33.181 -  41.240:  120   |   9:    73.476 -  81.535:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1092 r_free = 0.1563             target_work(ml) = 5.133         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1092 r_free = 0.1564             target_work(ml) = 5.133         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1092   r_free= 0.1564   ksol= 0.32   Bsol= 50.66   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.64,-2.15,-0.24,-0.00,-0.00,-0.00); trace/3= -1.68                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.132787                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9625 -  4.7269 0.99   1405  155 0.1016 0.1293      5.4107      5.5678|
|  2:  4.7269 -  3.7716 0.99   1352  151 0.0854 0.1140      5.4452      5.6511|
|  3:  3.7716 -  3.3007 0.99   1310  149 0.1046 0.1534      5.4721       5.844|
|  4:  3.3007 -  3.0016 0.99   1326  139 0.1168 0.1533      5.4211      5.5663|
|  5:  3.0016 -  2.7879 0.99   1296  149 0.1281 0.1601      5.3004      5.5237|
|  6:  2.7879 -  2.6245 0.99   1305  143 0.1202 0.1995      5.2012      5.4969|
|  7:  2.6245 -  2.4937 0.99   1284  147 0.1241 0.1650      5.1657      5.3371|
|  8:  2.4937 -  2.3856 0.98   1290  142 0.1101 0.1633      5.0605      5.3171|
|  9:  2.3856 -  2.2941 0.98   1285  139 0.1150 0.1880      5.0126      5.3394|
| 10:  2.2941 -  2.2152 0.99   1291  144 0.1096 0.1663      4.9278      5.1452|
| 11:  2.2152 -  2.1461 0.98   1274  143 0.1088 0.1756      4.9156       5.234|
| 12:  2.1461 -  2.0849 0.97   1262  139 0.1140 0.1615      4.8815      5.2162|
| 13:  2.0849 -  2.0302 0.99   1271  138 0.1016 0.1740      4.7412      4.9949|
| 14:  2.0302 -  1.9808 0.52    679   81 0.0858 0.1661      4.5662      4.9171|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9625 -  4.7269  1405   155  0.94   9.33   0.98     0.94       7367.63|
|  2:  4.7269 -  3.7716  1352   151  0.95   8.01   1.01     1.00       9403.66|
|  3:  3.7716 -  3.3007  1310   149  0.93  11.29   1.02     1.01      10394.58|
|  4:  3.3007 -  3.0016  1326   139  0.92  13.19   1.01     1.00       9806.89|
|  5:  3.0016 -  2.7879  1296   149  0.91  15.32   0.99     0.96       7908.21|
|  6:  2.7879 -  2.6245  1305   143  0.90  16.25   0.98     0.95       7041.97|
|  7:  2.6245 -  2.4937  1284   147  0.90  15.65   0.98     0.95       6303.91|
|  8:  2.4937 -  2.3856  1290   142  0.91  14.90   0.99     0.96       5384.38|
|  9:  2.3856 -  2.2941  1285   139  0.91  15.45   0.99     0.95       4850.20|
| 10:  2.2941 -  2.2152  1291   144  0.90  15.56   0.99     0.96       4217.31|
| 11:  2.2152 -  2.1461  1274   143  0.90  15.90   0.99     0.95       4275.92|
| 12:  2.1461 -  2.0849  1262   139  0.91  15.88   1.00     0.99       4023.65|
| 13:  2.0849 -  2.0302  1271   138  0.91  15.59   0.99     0.96       3164.78|
| 14:  2.0302 -  1.9808   679    81  0.94  12.19   0.97     0.94       2157.93|
|alpha:            min =        0.94 max =            1.01 mean =         0.97|
|beta:             min =     2157.93 max =        10394.58 mean =      6344.59|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.97 mean =        13.89|
|phase err.(test): min =        0.00 max =           89.79 mean =        13.46|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1091   r_free= 0.1556   ksol= 0.32   Bsol= 53.57   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.47,-1.99,-0.10,-0.00,-0.00,-0.00); trace/3= -1.52                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.129686                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1091   r_free= 0.1556   ksol= 0.32   Bsol= 53.57   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.47,-1.99,-0.10,-0.00,-0.00,-0.00); trace/3= -1.52                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.129686                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9625 -  4.7269 0.99   1405  155 0.1014 0.1245      5.3931      5.5314|
|  2:  4.7269 -  3.7716 0.99   1352  151 0.0858 0.1115      5.4345      5.6307|
|  3:  3.7716 -  3.3007 0.99   1310  149 0.1051 0.1516      5.4678      5.8306|
|  4:  3.3007 -  3.0016 0.99   1326  139 0.1167 0.1535      5.4177      5.5631|
|  5:  3.0016 -  2.7879 0.99   1296  149 0.1283 0.1597      5.2987      5.5206|
|  6:  2.7879 -  2.6245 0.99   1305  143 0.1200 0.1986      5.1983      5.4931|
|  7:  2.6245 -  2.4937 0.99   1284  147 0.1238 0.1653       5.164      5.3372|
|  8:  2.4937 -  2.3856 0.98   1290  142 0.1098 0.1635        5.06      5.3171|
|  9:  2.3856 -  2.2941 0.98   1285  139 0.1147 0.1888      5.0133      5.3428|
| 10:  2.2941 -  2.2152 0.99   1291  144 0.1096 0.1663      4.9292      5.1451|
| 11:  2.2152 -  2.1461 0.98   1274  143 0.1089 0.1756      4.9163      5.2349|
| 12:  2.1461 -  2.0849 0.97   1262  139 0.1139 0.1613       4.882      5.2157|
| 13:  2.0849 -  2.0302 0.99   1271  138 0.1014 0.1742      4.7409      4.9956|
| 14:  2.0302 -  1.9808 0.52    679   81 0.0858 0.1660      4.5659      4.9169|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9625 -  4.7269  1405   155  0.94   8.96   0.97     0.95       6950.85|
|  2:  4.7269 -  3.7716  1352   151  0.95   7.78   1.01     1.00       8926.41|
|  3:  3.7716 -  3.3007  1310   149  0.94  11.11   1.02     1.02      10072.46|
|  4:  3.3007 -  3.0016  1326   139  0.92  13.11   1.01     1.00       9692.88|
|  5:  3.0016 -  2.7879  1296   149  0.91  15.23   1.00     0.97       7843.36|
|  6:  2.7879 -  2.6245  1305   143  0.90  16.20   0.98     0.95       6986.08|
|  7:  2.6245 -  2.4937  1284   147  0.91  15.61   0.99     0.95       6276.51|
|  8:  2.4937 -  2.3856  1290   142  0.91  14.89   1.00     0.97       5389.94|
|  9:  2.3856 -  2.2941  1285   139  0.91  15.46   1.00     0.95       4868.12|
| 10:  2.2941 -  2.2152  1291   144  0.90  15.61   1.00     0.97       4238.12|
| 11:  2.2152 -  2.1461  1274   143  0.90  15.92   0.99     0.96       4283.88|
| 12:  2.1461 -  2.0849  1262   139  0.91  15.90   1.01     1.00       4032.45|
| 13:  2.0849 -  2.0302  1271   138  0.91  15.59   0.99     0.97       3165.25|
| 14:  2.0302 -  1.9808   679    81  0.94  12.19   0.98     0.95       2158.93|
|alpha:            min =        0.95 max =            1.02 mean =         0.97|
|beta:             min =     2158.93 max =        10072.46 mean =      6235.88|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.99 mean =        13.82|
|phase err.(test): min =        0.00 max =           89.76 mean =        13.36|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.879)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.91    81.50   16.46    None  None   None       |
|    all(noH): 2823   0      0.91    81.50   16.46    None  None   None       |
|    Sol.    : 438    0      3.97    79.10   38.48    None  None   None       |
|    Mac.    : 2385   0      0.91    81.50   12.41    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:     0.913 -   8.972:  884   |   5:    41.208 -  49.267:   94        |
|      1:     8.972 -  17.031: 1175   |   6:    49.267 -  57.325:   86        |
|      2:    17.031 -  25.090:  274   |   7:    57.325 -  65.384:   38        |
|      3:    25.090 -  33.149:  133   |   8:    65.384 -  73.443:   13        |
|      4:    33.149 -  41.208:  120   |   9:    73.443 -  81.502:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 279         
Filter by distance & map next to the model:
   mapped sites are within: 0.488 - 4.317
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 273 from: 279
   mapped sites are within: 0.703 - 4.317

peak=    5.393 closest distance to " NH2 ARG A  56 " =    2.175
peak=    5.331 closest distance to " O   HOH Z 142 " =    1.743
peak=    5.244 closest distance to " CB  ARG A 275 " =    0.931
peak=    5.229 closest distance to " NE2 GLN A  11 " =    1.163
peak=    5.149 closest distance to " CG  PRO A  54 " =    1.334
peak=    5.119 closest distance to " O   HOH Z 232 " =    2.371
peak=    4.954 closest distance to " O   HOH Z 126 " =    1.848
peak=    4.866 closest distance to " O   HOH Z 369 " =    2.297
peak=    4.856 closest distance to " CB  ARG A  79 " =    1.450
peak=    4.806 closest distance to " CB  GLN A 223 " =    1.472
peak=    4.715 closest distance to " CB  GLN A 183 " =    1.233
peak=    4.521 closest distance to " O   HOH Z  78 " =    1.726
peak=    4.516 closest distance to " CZ  PHE A 218 " =    1.096
peak=    4.504 closest distance to " CB  ARG A 190 " =    1.661
peak=    4.490 closest distance to " O   HOH Z  63 " =    2.030
peak=    4.481 closest distance to " O   HOH Z  40 " =    1.692
peak=    4.449 closest distance to " O   HOH Z 298 " =    1.871
peak=    4.444 closest distance to " CB  PRO A  54 " =    0.945
peak=    4.437 closest distance to " CG2 VAL A 257 " =    0.867
peak=    4.434 closest distance to " CB  VAL A 265 " =    1.264
peak=    4.420 closest distance to " ND2 ASN A 187 " =    1.476
peak=    4.362 closest distance to " CB  GLU A 152 " =    1.233
peak=    4.333 closest distance to " O   HOH Z 303 " =    2.136
peak=    4.316 closest distance to " O   HOH Z 427 " =    2.941
peak=    4.278 closest distance to " CA  TYR A  30 " =    0.910
peak=    4.273 closest distance to " CB  SER A  63 " =    1.169
peak=    4.252 closest distance to " O   HOH Z 250 " =    1.494
peak=    4.224 closest distance to " CD2 TRP A 179 " =    1.321
peak=    4.182 closest distance to " O   HOH Z 406 " =    1.658
peak=    4.168 closest distance to " CB  ASN A 148 " =    1.447
peak=    4.141 closest distance to " O   HOH Z  61 " =    1.673
peak=    4.129 closest distance to " O   HOH Z 272 " =    1.863
peak=    4.125 closest distance to " O   HOH Z 158 " =    3.113
peak=    4.119 closest distance to " O   HOH Z 313 " =    2.025
peak=    4.104 closest distance to " O   HOH Z 265 " =    2.278
peak=    4.095 closest distance to " O   SER A  87 " =    2.207
peak=    4.091 closest distance to " CG  PRO A 213 " =    1.220
peak=    4.090 closest distance to " OG  SER A  97 " =    2.902
peak=    4.089 closest distance to " CE  LYS A  76 " =    0.893
peak=    4.085 closest distance to " O   HOH Z 419 " =    2.253
peak=    4.053 closest distance to " O   HOH Z  15 " =    2.112
peak=    4.024 closest distance to " CA  ASN A 215 " =    1.048
peak=    3.993 closest distance to " C   PRO A 198 " =    1.449
peak=    3.980 closest distance to " O   HOH Z 346 " =    1.711
peak=    3.976 closest distance to " CG  PRO A  90 " =    1.217
peak=    3.970 closest distance to " CB  GLU A 277 " =    3.600
peak=    3.938 closest distance to " CB  ASN A 110 " =    1.129
peak=    3.929 closest distance to " NZ  LYS A 117 " =    3.210
peak=    3.925 closest distance to " CG  PRO A 198 " =    1.260
peak=    3.920 closest distance to " O   HOH Z 248 " =    1.592
peak=    3.902 closest distance to " O   HOH Z 209 " =    2.243
peak=    3.892 closest distance to " CB  TRP A 266 " =    1.034
peak=    3.877 closest distance to " CB  ASN A 142 " =    1.063
peak=    3.862 closest distance to " O   HOH Z 287 " =    2.047
peak=    3.860 closest distance to " CG  PRO A 243 " =    1.040
peak=    3.857 closest distance to " CB  TYR A 169 " =    0.703
peak=    3.845 closest distance to " N   TYR A 116 " =    1.556
peak=    3.829 closest distance to " CB  GLU A  46 " =    1.003
peak=    3.820 closest distance to " O   HOH Z 180 " =    2.200
peak=    3.806 closest distance to " O   HOH Z 392 " =    2.974
peak=    3.800 closest distance to " O   ASN A  74 " =    1.403
peak=    3.799 closest distance to " O   HOH Z 403 " =    1.474
peak=    3.797 closest distance to " O   HOH Z 368 " =    2.112
peak=    3.794 closest distance to " O   HOH Z  43 " =    1.878
peak=    3.787 closest distance to " O   HOH Z 133 " =    2.719
peak=    3.777 closest distance to " O   HOH Z 203 " =    1.653
peak=    3.772 closest distance to " O   HOH Z 368 " =    3.559
peak=    3.769 closest distance to " CG  LEU A 167 " =    1.296
peak=    3.761 closest distance to " O   HOH Z 193 " =    1.818
peak=    3.755 closest distance to " O   HOH Z 214 " =    2.089
peak=    3.754 closest distance to " O   HOH Z 423 " =    1.995
peak=    3.754 closest distance to " CD  LYS A 166 " =    1.210
peak=    3.754 closest distance to " CB  VAL A 202 " =    1.573
peak=    3.753 closest distance to " CB  LEU A 228 " =    1.076
peak=    3.752 closest distance to " CB  SER A 212 " =    1.192
peak=    3.748 closest distance to " O   HOH Z 402 " =    1.390
peak=    3.748 closest distance to " CG2AVAL A  72 " =    1.638
peak=    3.737 closest distance to " CB  ASP A 140 " =    1.068
peak=    3.732 closest distance to " OD1 ASN A  69 " =    2.603
peak=    3.729 closest distance to " O   HOH Z 148 " =    3.459
peak=    3.726 closest distance to " O   HOH Z  53 " =    2.492
peak=    3.721 closest distance to " CD  ARG A 159 " =    0.718
peak=    3.717 closest distance to " CA  SER A  87 " =    1.027
peak=    3.711 closest distance to " O   HOH Z 353 " =    2.640
peak=    3.711 closest distance to " O   HOH Z  68 " =    2.305
peak=    3.702 closest distance to " OG ASER A 258 " =    3.083
peak=    3.699 closest distance to " O   HOH Z 172 " =    3.227
peak=    3.697 closest distance to " O  BHOH Z 338 " =    2.322
peak=    3.697 closest distance to " O   HOH Z 337 " =    3.651
peak=    3.695 closest distance to " CA  THR A 264 " =    0.925
peak=    3.691 closest distance to " NH1AARG A 145 " =    1.271
peak=    3.689 closest distance to " O   HOH Z 234 " =    3.689
peak=    3.674 closest distance to " CG2 ILE A 120 " =    1.172
peak=    3.670 closest distance to " CA  ARG A  36 " =    1.010
peak=    3.660 closest distance to " O   HOH Z 126 " =    1.586
peak=    3.655 closest distance to " CZ  PHE A  38 " =    1.243
peak=    3.655 closest distance to " CG  MET A 185 " =    1.159
peak=    3.650 closest distance to " CB  GLN A  88 " =    1.220
peak=    3.646 closest distance to " N   ASN A  39 " =    1.249
peak=    3.640 closest distance to " O   HOH Z 294 " =    1.495
peak=    3.637 closest distance to " CB  ASN A  39 " =    0.884
peak=    3.632 closest distance to " O   HOH Z 213 " =    2.050
peak=    3.631 closest distance to " CG  GLN A  11 " =    1.882
peak=    3.620 closest distance to " CB  SER A   3 " =    1.259
peak=    3.611 closest distance to " O   HOH Z 285 " =    2.256
peak=    3.609 closest distance to " CB  LEU A  83 " =    0.792
peak=    3.609 closest distance to " ND2 ASN A 249 " =    0.895
peak=    3.609 closest distance to " O   HOH Z 128 " =    2.035
peak=    3.597 closest distance to " O   HOH Z  10 " =    1.809
peak=    3.596 closest distance to " CB  THR A  31 " =    1.561
peak=    3.587 closest distance to " CD  ARG A 269 " =    0.874
peak=    3.583 closest distance to " CZ3 TRP A 266 " =    1.114
peak=    3.582 closest distance to " O   HOH Z 261 " =    1.804
peak=    3.575 closest distance to " O   HOH Z 417 " =    3.415
peak=    3.573 closest distance to " OG BSER A 164 " =    2.305
peak=    3.572 closest distance to " CB  TYR A 169 " =    0.721
peak=    3.570 closest distance to " CE1 TYR A 186 " =    1.371
peak=    3.570 closest distance to " O   HOH Z 394 " =    3.940
peak=    3.566 closest distance to " CA  ARG A 195 " =    1.195
peak=    3.566 closest distance to " O   HOH Z  88 " =    2.506
peak=    3.547 closest distance to " CB  SER A  26 " =    1.731
peak=    3.536 closest distance to " O   HOH Z  97 " =    2.530
peak=    3.535 closest distance to " NE2 HIS A 207 " =    1.224
peak=    3.534 closest distance to " O   HOH Z 327 " =    1.555
peak=    3.533 closest distance to " O   HOH Z 128 " =    2.169
peak=    3.527 closest distance to " O   HOH Z 291 " =    1.519
peak=    3.515 closest distance to " O   HOH Z  21 " =    1.829
peak=    3.513 closest distance to " O   HOH Z  59 " =    1.870
peak=    3.506 closest distance to " CG  GLU A  37 " =    0.917
peak=    3.505 closest distance to " CA  ALA A  51 " =    0.919
peak=    3.502 closest distance to " CA  VAL A 125 " =    1.075
peak=    3.501 closest distance to " O   HOH Z  44 " =    2.904
peak=    3.492 closest distance to " CG1 VAL A 153 " =    0.989
peak=    3.487 closest distance to " CG  ARG A  66 " =    2.362
peak=    3.482 closest distance to " CB  PRO A  90 " =    1.097
peak=    3.477 closest distance to " O   HOH Z 365 " =    2.870
peak=    3.474 closest distance to " O   HOH Z 359 " =    1.569
peak=    3.471 closest distance to " O   HOH Z  44 " =    1.753
peak=    3.467 closest distance to " CD2 TYR A 186 " =    1.058
peak=    3.467 closest distance to " O   THR A 220 " =    1.342
peak=    3.460 closest distance to " O   HOH Z   1 " =    2.078
peak=    3.460 closest distance to " O   HOH Z   1 " =    1.620
peak=    3.456 closest distance to " CB  ARG A 139 " =    1.052
peak=    3.453 closest distance to " CD1 LEU A  96 " =    0.719
peak=    3.453 closest distance to " CB  LYS A 117 " =    1.200
peak=    3.446 closest distance to " CB  GLU A 128 " =    0.927
peak=    3.442 closest distance to " CB  TRP A 179 " =    1.464
peak=    3.440 closest distance to " O   HOH Z 257 " =    2.259
peak=    3.438 closest distance to " O   HOH Z 299 " =    4.317
peak=    3.437 closest distance to " CD  LYS A  76 " =    1.918
peak=    3.435 closest distance to " O   HOH Z 380 " =    1.673
peak=    3.435 closest distance to " O   HOH Z 280 " =    2.944
peak=    3.435 closest distance to " O   HOH Z 286 " =    2.307
peak=    3.434 closest distance to " O   HOH Z 421 " =    2.065
peak=    3.430 closest distance to " CG AARG A 275 " =    1.131
peak=    3.429 closest distance to " O   HOH Z 245 " =    1.332
peak=    3.424 closest distance to " N   PHE A 130 " =    1.259
peak=    3.415 closest distance to " CA  ALA A 233 " =    1.098
peak=    3.413 closest distance to " O   HOH Z 329 " =    4.142
peak=    3.413 closest distance to " O   HOH Z 147 " =    1.836
peak=    3.402 closest distance to " O   HOH Z 325 " =    2.451
peak=    3.392 closest distance to " CG  MET A 113 " =    1.122
peak=    3.390 closest distance to " CA  ILE A 234 " =    1.009
peak=    3.389 closest distance to " O   HOH Z 261 " =    1.862
peak=    3.384 closest distance to " CA  ASN A 217 " =    1.213
peak=    3.384 closest distance to " CA  TYR A 116 " =    1.325
peak=    3.381 closest distance to " O   ALA A   1 " =    1.657
peak=    3.380 closest distance to " O   HOH Z 273 " =    2.800
peak=    3.378 closest distance to " O   ALA A 165 " =    1.529
peak=    3.378 closest distance to " CB  PHE A 204 " =    0.738
peak=    3.377 closest distance to " O   HOH Z 389 " =    1.791
peak=    3.372 closest distance to " CB  ASN A 187 " =    1.035
peak=    3.372 closest distance to " OD2 ASP A 286 " =    3.224
peak=    3.369 closest distance to " N   ARG A 156 " =    1.374
peak=    3.365 closest distance to " O   HOH Z 163 " =    1.952
peak=    3.360 closest distance to " O   HOH Z 132 " =    2.499
peak=    3.357 closest distance to " OE1 GLN A  11 " =    2.155
peak=    3.354 closest distance to " CZ2 TRP A 179 " =    1.814
peak=    3.352 closest distance to " CG2 ILE A  20 " =    1.409
peak=    3.351 closest distance to " OG BSER A  99 " =    2.351
peak=    3.350 closest distance to " CA  ALA A 158 " =    1.318
peak=    3.342 closest distance to " CA  ASN A 127 " =    1.133
peak=    3.339 closest distance to " CB  ASN A 215 " =    1.129
peak=    3.335 closest distance to " O   HOH Z  66 " =    2.153
peak=    3.333 closest distance to " CD1 ILE A 199 " =    1.054
peak=    3.319 closest distance to " NZ  LYS A  48 " =    1.175
peak=    3.316 closest distance to " O   HOH Z 422 " =    2.621
peak=    3.316 closest distance to " CA  ARG A 159 " =    1.236
peak=    3.312 closest distance to " O   HOH Z 193 " =    1.690
peak=    3.307 closest distance to " CD1 LEU A 300 " =    1.233
peak=    3.306 closest distance to " O   HOH Z  97 " =    1.947
peak=    3.306 closest distance to " O   HOH Z 433 " =    1.796
peak=    3.299 closest distance to " CB  SER A 210 " =    0.759
peak=    3.295 closest distance to " O   HOH Z 305 " =    3.507
peak=    3.294 closest distance to " CB  MET A  47 " =    1.242
peak=    3.292 closest distance to " CB  ILE A 120 " =    1.241
peak=    3.289 closest distance to " O   HOH Z 258 " =    1.609
peak=    3.288 closest distance to " O   HOH Z 371 " =    2.869
peak=    3.288 closest distance to " CA  ALA A  84 " =    1.295
peak=    3.286 closest distance to " O   HOH Z  78 " =    2.162
peak=    3.284 closest distance to " O   HOH Z 371 " =    1.813
peak=    3.284 closest distance to " O   HOH Z  88 " =    2.957
peak=    3.283 closest distance to " O   HOH Z 233 " =    1.884
peak=    3.282 closest distance to " CB  TYR A 116 " =    0.769
peak=    3.280 closest distance to " CB  GLN A  89 " =    1.402
peak=    3.266 closest distance to " O   HOH Z 116 " =    3.019
peak=    3.263 closest distance to " O   HOH Z 171 " =    4.021
peak=    3.257 closest distance to " O   HOH Z 357 " =    2.030
peak=    3.253 closest distance to " O  BHOH Z  74 " =    1.256
peak=    3.251 closest distance to " CG1 VAL A 189 " =    1.981
peak=    3.246 closest distance to " O   HOH Z 251 " =    1.615
peak=    3.245 closest distance to " O   HOH Z   9 " =    2.009
peak=    3.244 closest distance to " O   HOH Z 234 " =    2.225
peak=    3.242 closest distance to " ND1 HIS A  86 " =    1.739
peak=    3.242 closest distance to " CB  ASP A 191 " =    1.222
peak=    3.238 closest distance to " O   HOH Z 193 " =    1.930
peak=    3.234 closest distance to " O   SER A 164 " =    1.281
peak=    3.226 closest distance to " CA  ALA A 291 " =    0.776
peak=    3.225 closest distance to " CD1 ILE A 106 " =    0.859
peak=    3.220 closest distance to " O   HOH Z 425 " =    2.027
peak=    3.219 closest distance to " NH2BARG A 145 " =    2.046
peak=    3.213 closest distance to " OG  SER A  22 " =    2.624
peak=    3.212 closest distance to " O   HOH Z 411 " =    3.867
peak=    3.212 closest distance to " CG2 THR A 221 " =    1.117
peak=    3.212 closest distance to " O   HOH Z 407 " =    2.428
peak=    3.212 closest distance to " CD1 LEU A 261 " =    1.226
peak=    3.212 closest distance to " CA  LYS A 117 " =    1.184
peak=    3.210 closest distance to " N   ASP A 162 " =    1.207
peak=    3.210 closest distance to " CA  ASP A 162 " =    1.033
peak=    3.209 closest distance to " O   HOH Z 173 " =    1.833
peak=    3.208 closest distance to " O   HOH Z 342 " =    1.093
peak=    3.204 closest distance to " CB  ALA A  34 " =    1.030
peak=    3.195 closest distance to " N   SER A 135 " =    1.266
peak=    3.193 closest distance to " CB  ALA A 114 " =    1.114
peak=    3.189 closest distance to " CA  ALA A 129 " =    1.358
peak=    3.188 closest distance to " CA  ARG A 139 " =    0.935
peak=    3.188 closest distance to " CB  ASP A 298 " =    1.139
peak=    3.188 closest distance to " O   MET A 105 " =    1.935
peak=    3.185 closest distance to " OH  TYR A 116 " =    1.062
peak=    3.183 closest distance to " CB  PRO A 243 " =    1.251
peak=    3.183 closest distance to " O   HOH Z  54 " =    1.629
peak=    3.177 closest distance to " CB  SER A 273 " =    0.855
peak=    3.176 closest distance to " CB  GLN A 103 " =    0.812
peak=    3.174 closest distance to " O   LEU A 228 " =    1.903
peak=    3.172 closest distance to " CB  LEU A 300 " =    0.919
peak=    3.167 closest distance to " O   HOH Z 185 " =    1.825
peak=    3.166 closest distance to " O   HOH Z 417 " =    1.980
peak=    3.162 closest distance to " CA  MET A 105 " =    1.011
peak=    3.159 closest distance to " OG BSER A 134 " =    2.951
peak=    3.159 closest distance to " OE2 GLU A  53 " =    1.953
peak=    3.158 closest distance to " CG1 ILE A  33 " =    1.208
peak=    3.145 closest distance to " O   HOH Z  94 " =    2.163
peak=    3.145 closest distance to " O   PHE A 192 " =    1.400
peak=    3.137 closest distance to " OG1 THR A 264 " =    0.733
peak=    3.129 closest distance to " CA  GLU A  46 " =    1.036
peak=    3.127 closest distance to " CG1 ILE A  49 " =    1.470
peak=    3.126 closest distance to " O   HOH Z 188 " =    1.909
peak=    3.119 closest distance to " OG ASER A  99 " =    1.347
peak=    3.119 closest distance to " O   HOH Z 426 " =    1.978
peak=    3.116 closest distance to " O   HOH Z  80 " =    1.584
peak=    3.114 closest distance to " CA  ALA A 154 " =    1.025
peak=    3.108 closest distance to " N   ASN A 127 " =    1.290
peak=    3.104 closest distance to " CB  ALA A   9 " =    1.590
peak=    3.100 closest distance to " O   PRO A  90 " =    1.592
peak=    3.082 closest distance to " CB  HIS A 108 " =    0.809
peak=    3.078 closest distance to " CG  GLN A  77 " =    2.116
peak=    3.075 closest distance to " CB  ALA A 248 " =    0.890
peak=    3.072 closest distance to " CB  ALA A 227 " =    1.100
peak=    3.062 closest distance to " NE  ARG A  79 " =    0.937
peak=    3.049 closest distance to " CG  LYS A  76 " =    0.921
peak=    3.048 closest distance to " O   HOH Z  47 " =    1.811
peak=    3.046 closest distance to " CB  SER A  62 " =    1.219
peak=    3.046 closest distance to " O   HOH Z 371 " =    3.150

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 192         
Filter by distance & map next to the model:
   mapped sites are within: 0.757 - 5.960
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 192 from: 192
   mapped sites are within: 0.757 - 5.960

peak=   -4.611 closest distance to " CD  ARG A  14 " =    3.510
peak=   -4.549 closest distance to " CD  GLN A  58 " =    0.984
peak=   -4.377 closest distance to " O   VAL A  67 " =    2.661
peak=   -4.372 closest distance to " C   HIS A 108 " =    1.123
peak=   -4.371 closest distance to " OG BSER A 134 " =    1.310
peak=   -4.365 closest distance to " CD  ARG A 156 " =    2.076
peak=   -4.299 closest distance to " O   PRO A 198 " =    1.246
peak=   -4.282 closest distance to " C   ILE A 239 " =    2.150
peak=   -4.256 closest distance to " CB  PRO A 243 " =    2.673
peak=   -4.114 closest distance to " O   HOH Z 266 " =    5.406
peak=   -4.090 closest distance to " CG  GLN A 223 " =    2.009
peak=   -4.075 closest distance to " CE  MET A 105 " =    2.486
peak=   -4.070 closest distance to " CD2 PHE A 192 " =    2.003
peak=   -4.058 closest distance to " CZ3 TRP A 179 " =    1.202
peak=   -4.054 closest distance to " O   HOH Z 231 " =    2.218
peak=   -4.018 closest distance to " CG1 VAL A 112 " =    2.872
peak=   -4.005 closest distance to " OXT GLY A 302 " =    2.800
peak=   -4.001 closest distance to " CG1 VAL A  67 " =    2.966
peak=   -3.961 closest distance to " CE BMET A  47 " =    1.307
peak=   -3.949 closest distance to " O   HOH Z 372 " =    2.254
peak=   -3.944 closest distance to " O   HOH Z 185 " =    2.305
peak=   -3.931 closest distance to " O   HOH Z 198 " =    1.566
peak=   -3.894 closest distance to " CA  ASP A 298 " =    1.111
peak=   -3.887 closest distance to " CD2 TYR A 293 " =    1.941
peak=   -3.884 closest distance to " O   HOH Z 211 " =    1.463
peak=   -3.879 closest distance to " OG  SER A  97 " =    2.254
peak=   -3.859 closest distance to " O   HOH Z 290 " =    1.243
peak=   -3.841 closest distance to " CG1 VAL A 112 " =    2.632
peak=   -3.805 closest distance to " CB  ASN A  39 " =    2.282
peak=   -3.757 closest distance to " CB  ALA A  43 " =    2.519
peak=   -3.751 closest distance to " O   SER A 210 " =    1.994
peak=   -3.742 closest distance to " N   ALA A 248 " =    1.592
peak=   -3.726 closest distance to " CE2 TYR A  30 " =    2.749
peak=   -3.720 closest distance to " O   HOH Z 351 " =    1.449
peak=   -3.704 closest distance to " CB  ALA A 291 " =    2.125
peak=   -3.698 closest distance to " ND2 ASN A  45 " =    1.797
peak=   -3.681 closest distance to " N   ALA A  43 " =    2.532
peak=   -3.678 closest distance to " OD1 ASP A 171 " =    1.658
peak=   -3.645 closest distance to " O   HOH Z 389 " =    1.986
peak=   -3.637 closest distance to " CG2 ILE A 263 " =    2.211
peak=   -3.628 closest distance to " O   HOH Z 313 " =    1.889
peak=   -3.626 closest distance to " O   HOH Z  15 " =    1.455
peak=   -3.618 closest distance to " CB  ALA A 161 " =    2.531
peak=   -3.617 closest distance to " CD1 LEU A 101 " =    2.307
peak=   -3.602 closest distance to " O   HOH Z 394 " =    1.469
peak=   -3.586 closest distance to " O   HOH Z  60 " =    1.877
peak=   -3.560 closest distance to " OD2 ASP A 191 " =    1.366
peak=   -3.556 closest distance to " CD1 ILE A 239 " =    2.461
peak=   -3.554 closest distance to " O   HOH Z 298 " =    1.306
peak=   -3.554 closest distance to " CG2 THR A 178 " =    2.298
peak=   -3.546 closest distance to " O   HOH Z 114 " =    3.055
peak=   -3.545 closest distance to " O   HOH Z  73 " =    2.410
peak=   -3.544 closest distance to " CD1 LEU A 255 " =    2.845
peak=   -3.541 closest distance to " O   HOH Z 196 " =    2.062
peak=   -3.533 closest distance to " OD1 ASN A 148 " =    1.464
peak=   -3.529 closest distance to " NH2AARG A 275 " =    5.277
peak=   -3.526 closest distance to " CD1 PHE A  59 " =    2.051
peak=   -3.523 closest distance to " O   HOH Z 429 " =    1.881
peak=   -3.522 closest distance to " O   SER A 135 " =    1.417
peak=   -3.518 closest distance to " O   ALA A  10 " =    1.643
peak=   -3.515 closest distance to " CZ  TYR A 169 " =    1.789
peak=   -3.514 closest distance to " O   HOH Z   6 " =    1.382
peak=   -3.513 closest distance to " ND2 ASN A 187 " =    1.488
peak=   -3.512 closest distance to " NH2 ARG A  79 " =    1.611
peak=   -3.511 closest distance to " CB  GLN A  11 " =    1.812
peak=   -3.511 closest distance to " CG  PHE A 283 " =    2.728
peak=   -3.505 closest distance to " O   GLN A 240 " =    2.101
peak=   -3.497 closest distance to " O   HOH Z 348 " =    2.222
peak=   -3.491 closest distance to " N   THR A 157 " =    1.532
peak=   -3.489 closest distance to " CB  ALA A 248 " =    2.330
peak=   -3.484 closest distance to " O   HOH Z 407 " =    2.976
peak=   -3.480 closest distance to " O   PHE A 218 " =    1.605
peak=   -3.477 closest distance to " ND2 ASN A  45 " =    1.154
peak=   -3.475 closest distance to " NE2 GLN A 278 " =    1.654
peak=   -3.460 closest distance to " CA  GLY A 241 " =    3.382
peak=   -3.452 closest distance to " O   SER A  95 " =    1.595
peak=   -3.446 closest distance to " CE2 PHE A  61 " =    2.577
peak=   -3.443 closest distance to " ND2 ASN A 249 " =    2.400
peak=   -3.440 closest distance to " CG1 VAL A 250 " =    2.624
peak=   -3.431 closest distance to " CB  ASP A 132 " =    2.273
peak=   -3.423 closest distance to " O   VAL A 189 " =    2.639
peak=   -3.421 closest distance to " O   HOH Z 174 " =    2.559
peak=   -3.416 closest distance to " O   HOH Z 131 " =    4.049
peak=   -3.413 closest distance to " CA  GLY A 241 " =    2.341
peak=   -3.412 closest distance to " O   HOH Z 102 " =    1.692
peak=   -3.409 closest distance to " CB  TRP A  85 " =    2.562
peak=   -3.406 closest distance to " O   HOH Z  38 " =    1.653
peak=   -3.406 closest distance to " O   MET A  40 " =    2.876
peak=   -3.405 closest distance to " CA  GLY A 203 " =    2.331
peak=   -3.404 closest distance to " O   HOH Z 191 " =    5.663
peak=   -3.396 closest distance to " O   HOH Z  37 " =    1.741
peak=   -3.393 closest distance to " OE2 GLU A 152 " =    1.259
peak=   -3.391 closest distance to " O   PRO A 163 " =    1.964
peak=   -3.377 closest distance to " O   HOH Z 395 " =    5.188
peak=   -3.376 closest distance to " O   HOH Z  11 " =    1.684
peak=   -3.376 closest distance to " O   HOH Z 359 " =    3.105
peak=   -3.373 closest distance to " O   HOH Z  10 " =    1.470
peak=   -3.370 closest distance to " C   LEU A 143 " =    0.984
peak=   -3.369 closest distance to " N   PHE A  59 " =    1.976
peak=   -3.367 closest distance to " O   HOH Z 421 " =    3.152
peak=   -3.362 closest distance to " OD2 ASP A 171 " =    2.353
peak=   -3.357 closest distance to " CG  TRP A 266 " =    1.970
peak=   -3.352 closest distance to " CG1 VAL A 125 " =    1.834
peak=   -3.339 closest distance to " CD  ARG A 139 " =    1.713
peak=   -3.339 closest distance to " CB  ALA A 291 " =    2.240
peak=   -3.333 closest distance to " OG BSER A 134 " =    1.792
peak=   -3.330 closest distance to " O   HOH Z 243 " =    1.865
peak=   -3.327 closest distance to " O   TYR A 247 " =    2.875
peak=   -3.324 closest distance to " CE3 TRP A 150 " =    2.278
peak=   -3.321 closest distance to " CG  ARG A 269 " =    2.319
peak=   -3.318 closest distance to " O   HOH Z 323 " =    1.482
peak=   -3.310 closest distance to " O   HOH Z 165 " =    2.006
peak=   -3.309 closest distance to " NH2BARG A 275 " =    1.967
peak=   -3.308 closest distance to " CG  LEU A  83 " =    1.945
peak=   -3.307 closest distance to " CG  GLU A 277 " =    1.273
peak=   -3.304 closest distance to " O   TRP A  70 " =    1.439
peak=   -3.298 closest distance to " O   HOH Z 362 " =    5.960
peak=   -3.298 closest distance to " O   HOH Z 166 " =    1.927
peak=   -3.297 closest distance to " C   MET A 188 " =    1.319
peak=   -3.294 closest distance to " CG1 VAL A 265 " =    2.638
peak=   -3.290 closest distance to " CE2 PHE A 218 " =    2.399
peak=   -3.290 closest distance to " O   VAL A 174 " =    2.119
peak=   -3.283 closest distance to " O   HOH Z 353 " =    2.233
peak=   -3.282 closest distance to " O   SER A  22 " =    2.503
peak=   -3.281 closest distance to " CG2 ILE A  49 " =    2.817
peak=   -3.281 closest distance to " N   GLN A  58 " =    1.744
peak=   -3.274 closest distance to " CD2 PHE A 192 " =    2.273
peak=   -3.270 closest distance to " O   HOH Z 174 " =    3.992
peak=   -3.269 closest distance to " CB  ASP A 286 " =    1.773
peak=   -3.267 closest distance to " CG  ARG A  66 " =    2.281
peak=   -3.267 closest distance to " O   HOH Z 317 " =    1.499
peak=   -3.266 closest distance to " CD  GLN A  88 " =    0.907
peak=   -3.265 closest distance to " O   VAL A 189 " =    1.692
peak=   -3.264 closest distance to " O   HOH Z 134 " =    3.360
peak=   -3.263 closest distance to " O   HOH Z  13 " =    1.785
peak=   -3.263 closest distance to " C   GLY A 262 " =    1.952
peak=   -3.262 closest distance to " CG1 VAL A  67 " =    3.198
peak=   -3.259 closest distance to " O   HOH Z 100 " =    1.232
peak=   -3.254 closest distance to " O   HOH Z 414 " =    1.512
peak=   -3.252 closest distance to " N   THR A  52 " =    1.747
peak=   -3.249 closest distance to " OH  TYR A 172 " =    1.848
peak=   -3.247 closest distance to " OE1 GLN A 183 " =    1.656
peak=   -3.237 closest distance to " O   ALA A 161 " =    1.693
peak=   -3.236 closest distance to " O   HOH Z 357 " =    2.078
peak=   -3.232 closest distance to " CB  ALA A 100 " =    2.197
peak=   -3.232 closest distance to " O   HOH Z  51 " =    1.707
peak=   -3.228 closest distance to " CG  ASP A 231 " =    0.757
peak=   -3.227 closest distance to " O   HOH Z 216 " =    1.333
peak=   -3.213 closest distance to " NH2 ARG A 159 " =    2.402
peak=   -3.207 closest distance to " O   ALA A 292 " =    2.083
peak=   -3.206 closest distance to " O   HOH Z 385 " =    2.010
peak=   -3.199 closest distance to " O   HOH Z 123 " =    2.514
peak=   -3.198 closest distance to " NE2 GLN A 194 " =    1.836
peak=   -3.196 closest distance to " O   GLY A  80 " =    2.475
peak=   -3.196 closest distance to " CD  GLN A 223 " =    0.923
peak=   -3.195 closest distance to " OE1 GLN A  88 " =    1.092
peak=   -3.193 closest distance to " CG  HIS A  86 " =    1.118
peak=   -3.189 closest distance to " ND2 ASN A  60 " =    1.325
peak=   -3.186 closest distance to " O   HOH Z 351 " =    1.359
peak=   -3.184 closest distance to " O   HOH Z 262 " =    2.894
peak=   -3.180 closest distance to " O   ARG A  24 " =    1.723
peak=   -3.179 closest distance to " CB  GLN A 223 " =    1.958
peak=   -3.173 closest distance to " O   HOH Z 281 " =    2.809
peak=   -3.162 closest distance to " O   HOH Z  63 " =    1.802
peak=   -3.161 closest distance to " O   GLY A  17 " =    1.083
peak=   -3.161 closest distance to " O   HOH Z 171 " =    1.995
peak=   -3.155 closest distance to " CA  GLY A  57 " =    2.136
peak=   -3.149 closest distance to " O   HOH Z 371 " =    1.700
peak=   -3.148 closest distance to " CE3 TRP A 274 " =    2.369
peak=   -3.148 closest distance to " CG1 VAL A 197 " =    2.177
peak=   -3.146 closest distance to " CG1 VAL A  67 " =    2.872
peak=   -3.146 closest distance to " N   ASN A 127 " =    1.470
peak=   -3.145 closest distance to " CE1 PHE A 218 " =    2.676
peak=   -3.145 closest distance to " CB  PRO A 163 " =    2.454
peak=   -3.144 closest distance to " CG2 VAL A 189 " =    2.086
peak=   -3.128 closest distance to " CB  TYR A  15 " =    2.273
peak=   -3.127 closest distance to " O   HOH Z 200 " =    3.006
peak=   -3.123 closest distance to " CA  GLY A 133 " =    2.087
peak=   -3.119 closest distance to " C   SER A 206 " =    1.502
peak=   -3.118 closest distance to " CD1 ILE A 106 " =    2.234
peak=   -3.118 closest distance to " O   PRO A 198 " =    1.282
peak=   -3.114 closest distance to " CD1 ILE A 199 " =    2.429
peak=   -3.107 closest distance to " CB  ASP A 132 " =    2.433
peak=   -3.104 closest distance to " CD2 PHE A 225 " =    1.137
peak=   -3.101 closest distance to " O   HOH Z 253 " =    3.834
peak=   -3.099 closest distance to " CG2 THR A 221 " =    2.234
peak=   -3.098 closest distance to " O   HOH Z 200 " =    4.540
peak=   -3.096 closest distance to " O   HOH Z  55 " =    1.049
peak=   -3.092 closest distance to " O   SER A 276 " =    1.687
peak=   -3.084 closest distance to " O   HOH Z 110 " =    1.369
peak=   -3.074 closest distance to " O   HOH Z  89 " =    2.841
peak=   -3.040 closest distance to " N   SER A 276 " =    1.308

================= 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    :  0.3669 0.3626   6.136129e+00   6.114123e+00
   1_bss:  0.3523 0.3484   6.113980e+00   6.088023e+00
   1_xyz:  0.2020 0.2299   5.615046e+00   5.713875e+00
   1_adp:  0.1860 0.2379   5.574355e+00   5.751757e+00
   1_occ:  0.1858 0.2373   5.572937e+00   5.750495e+00
   2_bss:  0.1820 0.2351   5.563163e+00   5.744058e+00
   2_xyz:  0.1411 0.1827   5.332080e+00   5.525689e+00
   2_adp:  0.1325 0.1775   5.278965e+00   5.488820e+00
   2_occ:  0.1324 0.1775   5.278350e+00   5.488360e+00
   3_bss:  0.1322 0.1770   5.276037e+00   5.485215e+00
   3_xyz:  0.1179 0.1622   5.182500e+00   5.413106e+00
   3_adp:  0.1155 0.1596   5.164817e+00   5.399710e+00
   3_occ:  0.1154 0.1596   5.164989e+00   5.400166e+00
   4_bss:  0.1153 0.1595   5.164770e+00   5.400203e+00
   4_xyz:  0.1099 0.1569   5.136797e+00   5.389151e+00
   4_adp:  0.1114 0.1552   5.139264e+00   5.379508e+00
   4_occ:  0.1113 0.1552   5.139007e+00   5.379733e+00
   5_bss:  0.1113 0.1553   5.139325e+00   5.380522e+00
   5_xyz:  0.1105 0.1561   5.138221e+00   5.385102e+00
   5_adp:  0.1092 0.1563   5.132697e+00   5.386923e+00
   5_occ:  0.1092 0.1564   5.132787e+00   5.387270e+00
   5_bss:  0.1091 0.1556   5.129686e+00   5.381356e+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  39.197  -2.291  -2.310   4.300  -0.000   0.000   0.000
   1_xyz:  0.321  39.197  -2.291  -2.310   4.300  -0.000   0.000   0.000
   1_adp:  0.321  39.197  -2.291  -2.310   4.300  -0.000   0.000   0.000
   1_occ:  0.321  39.197  -2.291  -2.310   4.300  -0.000   0.000   0.000
   2_bss:  0.329  55.876  -3.109  -2.681   0.545  -0.000   0.000   0.000
   2_xyz:  0.329  55.876  -3.109  -2.681   0.545  -0.000   0.000   0.000
   2_adp:  0.329  55.876  -3.109  -2.681   0.545  -0.000   0.000   0.000
   2_occ:  0.329  55.876  -3.109  -2.681   0.545  -0.000   0.000   0.000
   3_bss:  0.330  59.674  -2.924  -2.381  -0.068  -0.000  -0.000  -0.000
   3_xyz:  0.330  59.674  -2.924  -2.381  -0.068  -0.000  -0.000  -0.000
   3_adp:  0.330  59.674  -2.924  -2.381  -0.068  -0.000  -0.000  -0.000
   3_occ:  0.330  59.674  -2.924  -2.381  -0.068  -0.000  -0.000  -0.000
   4_bss:  0.330  59.674  -2.698  -2.207  -0.219  -0.000  -0.000  -0.000
   4_xyz:  0.330  59.674  -2.698  -2.207  -0.219  -0.000  -0.000  -0.000
   4_adp:  0.330  59.674  -2.698  -2.207  -0.219  -0.000  -0.000  -0.000
   4_occ:  0.330  59.674  -2.698  -2.207  -0.219  -0.000  -0.000  -0.000
   5_bss:  0.321  50.661  -2.637  -2.155  -0.240  -0.000  -0.000  -0.000
   5_xyz:  0.321  50.661  -2.637  -2.155  -0.240  -0.000  -0.000  -0.000
   5_adp:  0.321  50.661  -2.637  -2.155  -0.240  -0.000  -0.000  -0.000
   5_occ:  0.321  50.661  -2.637  -2.155  -0.240  -0.000  -0.000  -0.000
   5_bss:  0.322  53.570  -2.473  -1.992  -0.098  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  38.464 0.6637  0.8368    37412.053
   1_bss:  36.870 0.6807  0.8576    33695.629
   1_xyz:  21.906 0.8438  1.0057    13094.387
   1_adp:  23.078 0.8314  0.9974    14161.003
   1_occ:  23.057 0.8315  0.9976    14112.564
   2_bss:  22.632 0.8361  0.9473    13838.622
   2_xyz:  17.137 0.8880  0.9748     8438.710
   2_adp:  16.248 0.8961  0.9715     7916.509
   2_occ:  16.236 0.8962  0.9715     7906.181
   3_bss:  16.162 0.8969  0.9704     7839.656
   3_xyz:  14.582 0.9100  0.9782     6684.204
   3_adp:  14.238 0.9130  0.9722     6499.465
   3_occ:  14.245 0.9130  0.9721     6501.979
   4_bss:  14.241 0.9130  0.9752     6503.783
   4_xyz:  13.960 0.9154  0.9770     6346.281
   4_adp:  13.760 0.9171  0.9735     6282.039
   4_occ:  13.762 0.9171  0.9734     6280.442
   5_bss:  13.778 0.9170  0.9742     6287.756
   5_xyz:  13.824 0.9167  0.9742     6357.098
   5_adp:  13.845 0.9165  0.9680     6340.624
   5_occ:  13.850 0.9165  0.9679     6343.830
   5_bss:  13.774 0.9170  0.9727     6235.098
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.112   1.7247e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.112   1.7247e-01
   1_xyz:   1.227  0.009  0.080 15.538  0.005  4.113   8.3440e-02
   1_adp:   1.227  0.009  0.080 15.538  0.005  4.113   8.3440e-02
   1_occ:   1.227  0.009  0.080 15.538  0.005  4.113   8.3440e-02
   2_bss:   1.227  0.009  0.080 15.538  0.005  4.113   8.3440e-02
   2_xyz:   0.946  0.006  0.070 14.793  0.004  4.122   5.3315e-02
   2_adp:   0.946  0.006  0.070 14.793  0.004  4.122   5.3315e-02
   2_occ:   0.946  0.006  0.070 14.793  0.004  4.122   5.3315e-02
   3_bss:   0.946  0.006  0.070 14.793  0.004  4.122   5.3315e-02
   3_xyz:   0.991  0.007  0.075 14.734  0.004  4.127   5.8738e-02
   3_adp:   0.991  0.007  0.075 14.734  0.004  4.127   5.8738e-02
   3_occ:   0.991  0.007  0.075 14.734  0.004  4.127   5.8738e-02
   4_bss:   0.991  0.007  0.075 14.734  0.004  4.127   5.8738e-02
   4_xyz:   1.081  0.009  0.082 14.834  0.004  4.112   6.9474e-02
   4_adp:   1.081  0.009  0.082 14.834  0.004  4.112   6.9474e-02
   4_occ:   1.081  0.009  0.082 14.834  0.004  4.112   6.9474e-02
   5_bss:   1.081  0.009  0.082 14.834  0.004  4.112   6.9474e-02
   5_xyz:   1.046  0.009  0.081 14.694  0.004  4.114   6.6389e-02
   5_adp:   1.046  0.009  0.081 14.694  0.004  4.114   6.6389e-02
   5_occ:   1.046  0.009  0.081 14.694  0.004  4.114   6.6389e-02
   5_bss:   1.046  0.009  0.081 14.694  0.004  4.114   6.6389e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.399   2.4165e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.399   2.4165e-01
   1_xyz:   8.778  0.055  0.299 81.999  0.039  2.183   6.8604e-02
   1_adp:   8.778  0.055  0.299 81.999  0.039  2.183   6.8604e-02
   1_occ:   8.778  0.055  0.299 81.999  0.039  2.183   6.8604e-02
   2_bss:   8.778  0.055  0.299 81.999  0.039  2.183   6.8604e-02
   2_xyz:   6.388  0.033  0.223 83.836  0.038  2.368   4.1439e-02
   2_adp:   6.388  0.033  0.223 83.836  0.038  2.368   4.1439e-02
   2_occ:   6.388  0.033  0.223 83.836  0.038  2.368   4.1439e-02
   3_bss:   6.388  0.033  0.223 83.836  0.038  2.368   4.1439e-02
   3_xyz:   6.354  0.046  0.250 83.978  0.035  2.372   4.5921e-02
   3_adp:   6.354  0.046  0.250 83.978  0.035  2.372   4.5921e-02
   3_occ:   6.354  0.046  0.250 83.978  0.035  2.372   4.5921e-02
   4_bss:   6.354  0.046  0.250 83.978  0.035  2.372   4.5921e-02
   4_xyz:   6.975  0.052  0.277 82.561  0.037  2.316   5.2391e-02
   4_adp:   6.975  0.052  0.277 82.561  0.037  2.316   5.2391e-02
   4_occ:   6.975  0.052  0.277 82.561  0.037  2.316   5.2391e-02
   5_bss:   6.975  0.052  0.277 82.561  0.037  2.316   5.2391e-02
   5_xyz:   6.779  0.055  0.267 83.781  0.036  2.289   4.9916e-02
   5_adp:   6.779  0.055  0.267 83.781  0.036  2.289   4.9916e-02
   5_occ:   6.779  0.055  0.267 83.781  0.036  2.289   4.9916e-02
   5_bss:   6.779  0.055  0.267 83.781  0.036  2.289   4.9916e-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:  81.19   0.00  16.79  81.19   0.00  12.88  62.78   4.54  38.08
   1_occ:  81.19   0.00  16.79  81.19   0.00  12.88  62.78   4.54  38.08
   2_bss:  81.19   0.00  16.79  81.19   0.00  12.88  62.78   4.54  38.08
   2_xyz:  81.19   0.00  16.79  81.19   0.00  12.88  62.78   4.54  38.08
   2_adp:  73.43   0.00  17.22  73.43   0.00  12.97  73.27   5.73  40.32
   2_occ:  73.43   0.00  17.22  73.43   0.00  12.97  73.27   5.73  40.32
   3_bss:  73.43   0.00  17.22  73.43   0.00  12.97  73.27   5.73  40.32
   3_xyz:  73.43   0.00  17.22  73.43   0.00  12.97  73.27   5.73  40.32
   3_adp:  82.31   0.66  17.18  82.31   0.66  12.85  81.20   2.01  40.76
   3_occ:  82.31   0.66  17.18  82.31   0.66  12.85  81.20   2.01  40.76
   4_bss:  82.31   0.66  17.18  82.31   0.66  12.85  81.20   2.01  40.76
   4_xyz:  82.31   0.66  17.18  82.31   0.66  12.85  81.20   2.01  40.76
   4_adp:  77.13   1.78  16.29  77.13   1.78  12.50  74.72   3.08  36.91
   4_occ:  77.13   1.78  16.29  77.13   1.78  12.50  74.72   3.08  36.91
   5_bss:  77.13   1.78  16.29  77.13   1.78  12.50  74.72   3.08  36.91
   5_xyz:  77.13   1.78  16.29  77.13   1.78  12.50  74.72   3.08  36.91
   5_adp:  81.53   0.95  16.49  81.53   0.95  12.45  79.13   4.00  38.52
   5_occ:  81.53   0.95  16.49  81.53   0.95  12.45  79.13   4.00  38.52
   5_bss:  81.50   0.91  16.46  81.50   0.91  12.41  79.10   3.97  38.48
------------------------------------------------------------------------
 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:    1.642    0.022    0.369
   1_adp:    1.642    0.022    0.369
   1_occ:    1.642    0.022    0.369
   2_bss:    1.642    0.022    0.369
   2_xyz:    1.190    0.033    0.411
   2_adp:    1.190    0.033    0.411
   2_occ:    1.190    0.033    0.411
   3_bss:    1.190    0.033    0.411
   3_xyz:    1.032    0.022    0.454
   3_adp:    1.032    0.022    0.454
   3_occ:    1.032    0.022    0.454
   4_bss:    1.032    0.022    0.454
   4_xyz:    1.377    0.066    0.469
   4_adp:    1.377    0.066    0.469
   4_occ:    1.377    0.066    0.469
   5_bss:    1.377    0.066    0.469
   5_xyz:    1.537    0.081    0.478
   5_adp:    1.537    0.081    0.478
   5_occ:    1.537    0.081    0.478
   5_bss:    1.537    0.081    0.478
------------------------------------------------------------------------

CPU time actual refinement: 329.36


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_416/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_416/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_416/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_416/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_416/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 329.21 
  Macro-tasks:
    bulk solvent and scale       = 35.93  
    individual site refinement   = 139.20 
    weights calculation          = 29.06  
    collect and process          = 6.51   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 210.81 
  Micro-tasks:
    mask                            = 1.87   
    f_calc                          = 105.68 
    alpha_beta                      = 8.01   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 115.60 
    fmodel                         = 6.48   
    r_factors                      = 0.15   
    phase_errors                   = 10.77  
    foms                           = 0.29   
    TOTAL for micro-tasks          = 250.01 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.606 micro seconds
Total CPU time: 5.71 minutes
from_scatterers_fft:    662 calls, 105.29 s
gradients_fft:          607 calls, 101.32 s

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

# Date 2008-01-16 Time 04:46:31 PST -0800 (1200487591.18 s)
Start R-work = 0.3669, R-free = 0.3626 (no bulk solvent and anisotropic scale)
Final R-work = 0.1324, R-free = 0.1750 (no bulk solvent and anisotropic scale)

Start R-work = 0.3523, R-free = 0.3484
Final R-work = 0.1091, R-free = 0.1556