# Date 2008-01-16 Time 04:39:03 PST -0800 (1200487143.20 s)
#phil __OFF__

Command line arguments: "../407.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 8510
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 407

-------------------------------------------------------------------------------
  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, 84.2302, 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: 3.24, per 1000 atoms: 1.15


================================== 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, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.782 1.95122
Completeness in resolution range: 0.954723
Completeness with d_max=infinity: 0.951754

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.7820
                             d_min =   1.9512

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, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.782 1.95122
Completeness in resolution range: 0.954723
Completeness with d_max=infinity: 0.951754

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.7824 -  4.1752 [2152/2180]  1940   212   9.9%
  bin  2:  4.1752 -  3.3264 [2069/2088]  1859   210  10.1%
  bin  3:  3.3264 -  2.9095 [2045/2065]  1841   204  10.0%
  bin  4:  2.9095 -  2.6452 [2034/2059]  1835   199   9.8%
  bin  5:  2.6452 -  2.4565 [2012/2032]  1807   205  10.2%
  bin  6:  2.4565 -  2.3122 [2002/2048]  1803   199   9.9%
  bin  7:  2.3122 -  2.1968 [1973/2005]  1773   200  10.1%
  bin  8:  2.1968 -  2.1015 [1988/2024]  1789   199  10.0%
  bin  9:  2.1015 -  2.0208 [1994/2024]  1798   196   9.8%
  bin 10:  2.0208 -  1.9512 [1320/1993]  1185   135  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_407/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: 0.14 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:
        1.43 -     2.12: 24
        2.12 -     2.82: 900
        2.82 -     3.51: 4542
        3.51 -     4.21: 9498
        4.21 -     4.90: 13958
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 178 " - " O   HOH Z 403 "  1.429 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.482 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.735 3.040 -x+1/2,-y+1,z+1/2
  " NH2 ARG A 259 " - " O   HOH Z   3 "  1.744 3.120 -x,y-1/2,-z+1/2
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.750 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28917 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_407/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_407/model_refine_001.geo

CPU time processing inputs: 9.07


============================ 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 84.23025 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: 1.95 - 14.78 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3998   r_free= 0.3994   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:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.192830                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7824 -  4.6568 0.99   1395  154 0.3298 0.3317      6.4724       6.451|
|  2:  4.6568 -  3.7155 0.99   1358  148 0.3312 0.3126      6.6488       6.623|
|  3:  3.7155 -  3.2516 0.99   1312  153 0.3624 0.3720       6.545      6.6923|
|  4:  3.2516 -  2.9569 0.99   1324  143 0.3662 0.3987       6.396      6.4289|
|  5:  2.9569 -  2.7464 0.99   1303  145 0.4100 0.3966      6.2809      6.2542|
|  6:  2.7464 -  2.5854 0.98   1288  144 0.4285 0.4309       6.178      6.1572|
|  7:  2.5854 -  2.4565 0.99   1302  143 0.4275 0.3793      6.1647      6.1024|
|  8:  2.4565 -  2.3500 0.98   1275  145 0.4320 0.4444       6.106      6.1228|
|  9:  2.3500 -  2.2599 0.98   1298  143 0.4492 0.4215      6.0632      6.0296|
| 10:  2.2599 -  2.1821 0.98   1271  136 0.4468 0.4738      6.0314      6.0807|
| 11:  2.1821 -  2.1141 0.99   1271  146 0.4665 0.4808      5.9984      6.0427|
| 12:  2.1141 -  2.0538 0.98   1276  139 0.4497 0.4366      5.9173      5.9297|
| 13:  2.0538 -  1.9999 0.97   1264  140 0.4586 0.4778      5.8323       5.814|
| 14:  1.9999 -  1.9512 0.54    693   80 0.4935 0.4498      5.8167      5.6935|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7824 -  4.6568  1395   154  0.74  30.91   0.86     0.76      57240.52|
|  2:  4.6568 -  3.7155  1358   148  0.76  29.52   0.95     0.87      78251.47|
|  3:  3.7155 -  3.2516  1312   153  0.69  36.33   0.97     0.89      83023.10|
|  4:  3.2516 -  2.9569  1324   143  0.63  41.51   0.99     0.85      74209.31|
|  5:  2.9569 -  2.7464  1303   145  0.57  46.31   0.95     0.80      60099.62|
|  6:  2.7464 -  2.5854  1288   144  0.56  47.31   0.94     0.78      51132.29|
|  7:  2.5854 -  2.4565  1302   143  0.57  46.15   0.97     0.78      45777.20|
|  8:  2.4565 -  2.3500  1275   145  0.55  48.40   0.97     0.77      41689.21|
|  9:  2.3500 -  2.2599  1298   143  0.53  49.92   1.00     0.74      38621.67|
| 10:  2.2599 -  2.1821  1271   136  0.51  51.49   1.01     0.72      37322.26|
| 11:  2.1821 -  2.1141  1271   146  0.48  53.41   1.01     0.71      35787.88|
| 12:  2.1141 -  2.0538  1276   139  0.49  53.14   1.03     0.75      33853.06|
| 13:  2.0538 -  1.9999  1264   140  0.48  53.94   1.00     0.72      28824.23|
| 14:  1.9999 -  1.9512   693    80  0.49  53.18   0.98     0.68      23033.32|
|alpha:            min =        0.68 max =            0.89 mean =         0.78|
|beta:             min =    23033.32 max =        83023.10 mean =     50417.79|
|figures of merit: min =        0.00 max =            1.00 mean =         0.58|
|phase err.(work): min =        0.00 max =           89.99 mean =        45.37|
|phase err.(test): min =        0.00 max =           89.22 mean =        45.45|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.555118              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.996   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.311886              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.785   (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 |  1.429 -  1.776:        6 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.776 -  2.123:       18 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.123 -  2.470:       30 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.470 -  2.817:      870 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.817 -  3.164:     2101 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.164 -  3.511:     2441 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.511 -  3.859:     4688 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.859 -  4.206:     4810 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.206 -  4.553:     6323 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.553 -  4.900:     7635 |
|-----------------------------------------------------------------------------|
|-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 |        0.187 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.109    4.900  1.429 |       0.588 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.430)------------------------------------------|
|    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: 1.95 - 14.78 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3998   r_free= 0.3994   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:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.192830                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.78 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3861   r_free= 0.3816   ksol= 0.32   Bsol= 20.00   scale= 0.965   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.35,-2.28,3.41,-0.00,0.00,0.00); trace/3= -0.41                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.180470                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.389666              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.973   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.656034              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.777   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3861      final r-factor (work) = 0.2760          |
| start r-factor (free) = 0.3816      final r-factor (free) = 0.2995          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.7486 = 4.39 * 0.50 * 6.1788 + 1.00 * 0.1872                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.2667 = 4.39 * 0.50 * 6.0034 + 1.00 * 0.0901                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2760      final r-factor (work) = 0.2527          |
| start r-factor (free) = 0.2995      final r-factor (free) = 0.3068          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9444 = 0.66 * 1.00 * 6.0034 + 1.00 * 0.0059                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8479 = 0.66 * 1.00 * 5.8460 + 1.00 * 0.0127                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.430)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.45   18.11    None  None   None       |
|    all(noH): 2823   0      0.00    83.45   18.11    None  None   None       |
|    Sol.    : 438    0      2.35    79.60   39.50    None  None   None       |
|    Mac.    : 2385   0      0.00    83.45   14.18    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 -   8.345:  688   |   5:    41.727 -  50.072:  103        |
|      1:     8.345 -  16.691: 1080   |   6:    50.072 -  58.417:   67        |
|      2:    16.691 -  25.036:  433   |   7:    58.417 -  66.763:   42        |
|      3:    25.036 -  33.381:  212   |   8:    66.763 -  75.108:   17        |
|      4:    33.381 -  41.727:  172   |   9:    75.108 -  83.454:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2527 r_free = 0.3068             target_work(ml) = 5.855         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2525 r_free = 0.3070             target_work(ml) = 5.854         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.78 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2525   r_free= 0.3070   ksol= 0.32   Bsol= 20.00   scale= 1.030   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.35,-2.28,3.41,-0.00,0.00,0.00); trace/3= -0.41                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.854489                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.78 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2497   r_free= 0.3053   ksol= 0.32   Bsol= 33.47   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.55,-2.06,0.61,-0.00,0.00,0.00); trace/3= -1.33                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.848330                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.057994              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.032   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.195868              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 147.189  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2497      final r-factor (work) = 0.1854          |
| start r-factor (free) = 0.3053      final r-factor (free) = 0.2372          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.0246 = 3.06 * 0.50 * 5.8433 + 1.00 * 0.0901                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.8141 = 3.06 * 0.50 * 5.7238 + 1.00 * 0.0624                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1854      final r-factor (work) = 0.1742          |
| start r-factor (free) = 0.2372      final r-factor (free) = 0.2215          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1336 = 0.20 * 1.00 * 5.7238 + 1.00 * 0.0125                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0955 = 0.20 * 1.00 * 5.5563 + 1.00 * 0.0072                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.430)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.92    83.05   17.40    None  None   None       |
|    all(noH): 2823   0      0.92    83.05   17.40    None  None   None       |
|    Sol.    : 438    0      6.52    74.50   38.24    None  None   None       |
|    Mac.    : 2385   0      0.92    83.05   13.57    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.920 -   9.133:  734   |   5:    41.985 -  50.199:  119        |
|      1:     9.133 -  17.346: 1212   |   6:    50.199 -  58.412:   57        |
|      2:    17.346 -  25.559:  348   |   7:    58.412 -  66.625:   24        |
|      3:    25.559 -  33.772:  163   |   8:    66.625 -  74.838:   15        |
|      4:    33.772 -  41.985:  148   |   9:    74.838 -  83.051:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1742 r_free = 0.2215             target_work(ml) = 5.523         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1736 r_free = 0.2215             target_work(ml) = 5.522         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.78 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1736   r_free= 0.2215   ksol= 0.32   Bsol= 33.47   scale= 1.036   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.55,-2.06,0.61,-0.00,0.00,0.00); trace/3= -1.33                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.521703                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.78 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1730   r_free= 0.2205   ksol= 0.32   Bsol= 33.47   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.80,-2.46,-1.14,-0.00,-0.00,-0.00); trace/3= -2.13                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.516192                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.817340              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.092  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.921334              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.485  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1730      final r-factor (work) = 0.1379          |
| start r-factor (free) = 0.2205      final r-factor (free) = 0.1791          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1117 = 1.82 * 0.50 * 5.5568 + 1.00 * 0.0624                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.9679 = 1.82 * 0.50 * 5.4139 + 1.00 * 0.0485                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1379      final r-factor (work) = 0.1285          |
| start r-factor (free) = 0.1791      final r-factor (free) = 0.1729          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.9953 = 0.92 * 1.00 * 5.4139 + 1.00 * 0.0073                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.8678 = 0.92 * 1.00 * 5.2734 + 1.00 * 0.0092                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.430)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.65   17.82    None  None   None       |
|    all(noH): 2823   0      0.00    92.65   17.82    None  None   None       |
|    Sol.    : 438    0      6.61    81.57   41.99    None  None   None       |
|    Mac.    : 2385   0      0.00    92.65   13.38    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 -   9.265:  787   |   5:    46.325 -  55.590:  112        |
|      1:     9.265 -  18.530: 1285   |   6:    55.590 -  64.855:   69        |
|      2:    18.530 -  27.795:  277   |   7:    64.855 -  74.120:   27        |
|      3:    27.795 -  37.060:  119   |   8:    74.120 -  83.385:   12        |
|      4:    37.060 -  46.325:  132   |   9:    83.385 -  92.650:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1285 r_free = 0.1729             target_work(ml) = 5.254         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1284 r_free = 0.1728             target_work(ml) = 5.254         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.78 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1284   r_free= 0.1728   ksol= 0.32   Bsol= 33.47   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.80,-2.46,-1.14,-0.00,-0.00,-0.00); trace/3= -2.13                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.253897                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.78 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1287   r_free= 0.1728   ksol= 0.32   Bsol= 36.59   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.92,-2.54,-1.81,-0.00,-0.00,-0.00); trace/3= -2.42                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.253293                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.724759              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 114.793  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.430949              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 122.380  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1287      final r-factor (work) = 0.1163          |
| start r-factor (free) = 0.1728      final r-factor (free) = 0.1609          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.5973 = 1.72 * 0.50 * 5.2748 + 1.00 * 0.0485                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.5439 = 1.72 * 0.50 * 5.2088 + 1.00 * 0.0519                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1163      final r-factor (work) = 0.1140          |
| start r-factor (free) = 0.1609      final r-factor (free) = 0.1589          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2539 = 0.43 * 1.00 * 5.2088 + 1.00 * 0.0092                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2318 = 0.43 * 1.00 * 5.1586 + 1.00 * 0.0087                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.430)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.60    94.89   17.50    None  None   None       |
|    all(noH): 2823   0      1.60    94.89   17.50    None  None   None       |
|    Sol.    : 438    0      6.39    83.95   41.04    None  None   None       |
|    Mac.    : 2385   0      1.60    94.89   13.18    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:     1.597 -  10.926: 1213   |   5:    48.245 -  57.574:  103        |
|      1:    10.926 -  20.256:  968   |   6:    57.574 -  66.904:   52        |
|      2:    20.256 -  29.585:  207   |   7:    66.904 -  76.233:   22        |
|      3:    29.585 -  38.915:  129   |   8:    76.233 -  85.563:    6        |
|      4:    38.915 -  48.245:  119   |   9:    85.563 -  94.892:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1140 r_free = 0.1589             target_work(ml) = 5.151         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1139 r_free = 0.1587             target_work(ml) = 5.151         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.78 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1139   r_free= 0.1587   ksol= 0.32   Bsol= 36.59   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.92,-2.54,-1.81,-0.00,-0.00,-0.00); trace/3= -2.42                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.150610                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.78 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1139   r_free= 0.1587   ksol= 0.32   Bsol= 36.59   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.80,-2.39,-1.87,-0.00,-0.00,-0.00); trace/3= -2.35                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.150583                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.608539              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 145.463  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.409935              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.287  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1139      final r-factor (work) = 0.1074          |
| start r-factor (free) = 0.1587      final r-factor (free) = 0.1554          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7800 = 2.61 * 0.50 * 5.1585 + 1.00 * 0.0519                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7473 = 2.61 * 0.50 * 5.1255 + 1.00 * 0.0623                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1074      final r-factor (work) = 0.1067          |
| start r-factor (free) = 0.1554      final r-factor (free) = 0.1549          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1098 = 0.41 * 1.00 * 5.1255 + 1.00 * 0.0087                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1039 = 0.41 * 1.00 * 5.1117 + 1.00 * 0.0084                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.430)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.73    96.92   17.20    None  None   None       |
|    all(noH): 2823   0      1.73    96.92   17.20    None  None   None       |
|    Sol.    : 438    0      6.08    82.88   40.07    None  None   None       |
|    Mac.    : 2385   0      1.73    96.92   13.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.732 -  11.250: 1312   |   5:    49.325 -  58.844:   93        |
|      1:    11.250 -  20.769:  909   |   6:    58.844 -  68.363:   41        |
|      2:    20.769 -  30.288:  189   |   7:    68.363 -  77.881:   19        |
|      3:    30.288 -  39.807:  137   |   8:    77.881 -  87.400:    4        |
|      4:    39.807 -  49.325:  115   |   9:    87.400 -  96.919:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1067 r_free = 0.1549             target_work(ml) = 5.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1067 r_free = 0.1548             target_work(ml) = 5.109         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.78 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1067   r_free= 0.1548   ksol= 0.32   Bsol= 36.59   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.80,-2.39,-1.87,-0.00,-0.00,-0.00); trace/3= -2.35                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.109433                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7824 -  4.6568 0.99   1395  154 0.0974 0.1236      5.3564      5.5067|
|  2:  4.6568 -  3.7155 0.99   1358  148 0.0820 0.1108      5.3985      5.6005|
|  3:  3.7155 -  3.2516 0.99   1312  153 0.1024 0.1490       5.441       5.824|
|  4:  3.2516 -  2.9569 0.99   1324  143 0.1170 0.1602      5.4277      5.6102|
|  5:  2.9569 -  2.7464 0.99   1303  145 0.1193 0.1591       5.255      5.4319|
|  6:  2.7464 -  2.5854 0.98   1288  144 0.1153 0.1714      5.1503       5.376|
|  7:  2.5854 -  2.4565 0.99   1302  143 0.1148 0.1585      5.0925      5.3302|
|  8:  2.4565 -  2.3500 0.98   1275  145 0.1085 0.1710      5.0251      5.2962|
|  9:  2.3500 -  2.2599 0.98   1298  143 0.1129 0.1813           5      5.3038|
| 10:  2.2599 -  2.1821 0.98   1271  136 0.1088 0.1734      4.9418       5.195|
| 11:  2.1821 -  2.1141 0.99   1271  146 0.1097 0.1732       4.912      5.2651|
| 12:  2.1141 -  2.0538 0.98   1276  139 0.1031 0.1636      4.8265      5.0799|
| 13:  2.0538 -  1.9999 0.97   1264  140 0.1093 0.1777      4.7665      5.0594|
| 14:  1.9999 -  1.9512 0.54    693   80 0.1055 0.1582      4.6684      4.8711|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7824 -  4.6568  1395   154  0.94   8.47   0.99     0.96       6389.81|
|  2:  4.6568 -  3.7155  1358   148  0.96   7.43   1.03     1.02       8339.85|
|  3:  3.7155 -  3.2516  1312   153  0.94  11.00   1.04     1.04       9792.23|
|  4:  3.2516 -  2.9569  1324   143  0.92  13.33   1.02     1.00       9931.17|
|  5:  2.9569 -  2.7464  1303   145  0.91  14.78   1.00     0.97       7297.97|
|  6:  2.7464 -  2.5854  1288   144  0.91  15.04   0.99     0.97       6282.79|
|  7:  2.5854 -  2.4565  1302   143  0.92  14.08   1.00     0.96       5336.64|
|  8:  2.4565 -  2.3500  1275   145  0.91  14.76   1.00     0.99       5072.96|
|  9:  2.3500 -  2.2599  1298   143  0.91  14.92   1.01     0.99       4719.00|
| 10:  2.2599 -  2.1821  1271   136  0.91  15.28   1.01     0.98       4321.83|
| 11:  2.1821 -  2.1141  1271   146  0.90  16.26   1.01     0.98       4243.03|
| 12:  2.1141 -  2.0538  1276   139  0.92  14.40   1.01     0.99       3629.74|
| 13:  2.0538 -  1.9999  1264   140  0.90  15.74   1.01     1.01       3222.25|
| 14:  1.9999 -  1.9512   693    80  0.91  15.14   1.00     0.97       2569.14|
|alpha:            min =        0.96 max =            1.04 mean =         0.99|
|beta:             min =     2569.14 max =         9931.17 mean =      5941.55|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.57 mean =        13.50|
|phase err.(test): min =        0.00 max =           88.86 mean =        13.12|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.78 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1066   r_free= 0.1548   ksol= 0.32   Bsol= 37.58   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.62,-2.22,-1.75,-0.00,-0.00,-0.00); trace/3= -2.20                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.109509                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.78 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1066   r_free= 0.1548   ksol= 0.32   Bsol= 37.58   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.62,-2.22,-1.75,-0.00,-0.00,-0.00); trace/3= -2.20                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.109509                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7824 -  4.6568 0.99   1395  154 0.0975 0.1239      5.3587      5.5099|
|  2:  4.6568 -  3.7155 0.99   1358  148 0.0821 0.1108      5.3994      5.6004|
|  3:  3.7155 -  3.2516 0.99   1312  153 0.1024 0.1490      5.4411      5.8243|
|  4:  3.2516 -  2.9569 0.99   1324  143 0.1170 0.1602      5.4277      5.6102|
|  5:  2.9569 -  2.7464 0.99   1303  145 0.1192 0.1591      5.2548      5.4314|
|  6:  2.7464 -  2.5854 0.98   1288  144 0.1153 0.1715      5.1502      5.3763|
|  7:  2.5854 -  2.4565 0.99   1302  143 0.1148 0.1584      5.0924        5.33|
|  8:  2.4565 -  2.3500 0.98   1275  145 0.1085 0.1708      5.0248      5.2958|
|  9:  2.3500 -  2.2599 0.98   1298  143 0.1129 0.1814      4.9998      5.3043|
| 10:  2.2599 -  2.1821 0.98   1271  136 0.1087 0.1733      4.9415       5.194|
| 11:  2.1821 -  2.1141 0.99   1271  146 0.1096 0.1730      4.9117      5.2648|
| 12:  2.1141 -  2.0538 0.98   1276  139 0.1031 0.1635       4.826      5.0797|
| 13:  2.0538 -  1.9999 0.97   1264  140 0.1092 0.1776       4.766      5.0582|
| 14:  1.9999 -  1.9512 0.54    693   80 0.1055 0.1582      4.6682      4.8716|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7824 -  4.6568  1395   154  0.94   8.50   0.99     0.96       6443.09|
|  2:  4.6568 -  3.7155  1358   148  0.96   7.45   1.03     1.02       8368.50|
|  3:  3.7155 -  3.2516  1312   153  0.94  11.00   1.04     1.04       9792.83|
|  4:  3.2516 -  2.9569  1324   143  0.92  13.33   1.02     1.00       9930.39|
|  5:  2.9569 -  2.7464  1303   145  0.91  14.78   1.00     0.98       7297.50|
|  6:  2.7464 -  2.5854  1288   144  0.91  15.04   0.99     0.97       6281.62|
|  7:  2.5854 -  2.4565  1302   143  0.92  14.08   1.00     0.97       5334.98|
|  8:  2.4565 -  2.3500  1275   145  0.91  14.76   1.00     0.99       5069.52|
|  9:  2.3500 -  2.2599  1298   143  0.91  14.91   1.02     0.99       4716.78|
| 10:  2.2599 -  2.1821  1271   136  0.91  15.28   1.01     0.98       4319.26|
| 11:  2.1821 -  2.1141  1271   146  0.90  16.26   1.02     0.99       4239.70|
| 12:  2.1141 -  2.0538  1276   139  0.92  14.39   1.02     0.99       3625.07|
| 13:  2.0538 -  1.9999  1264   140  0.90  15.73   1.02     1.02       3218.68|
| 14:  1.9999 -  1.9512   693    80  0.91  15.14   1.01     0.97       2567.51|
|alpha:            min =        0.96 max =            1.04 mean =         0.99|
|beta:             min =     2567.51 max =         9930.39 mean =      5946.22|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.58 mean =        13.50|
|phase err.(test): min =        0.00 max =           88.87 mean =        13.12|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.430)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.67    96.86   17.14    None  None   None       |
|    all(noH): 2823   0      1.67    96.86   17.14    None  None   None       |
|    Sol.    : 438    0      6.02    82.82   40.01    None  None   None       |
|    Mac.    : 2385   0      1.67    96.86   12.94    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:     1.670 -  11.188: 1312   |   5:    49.263 -  58.782:   93        |
|      1:    11.188 -  20.707:  909   |   6:    58.782 -  68.301:   41        |
|      2:    20.707 -  30.226:  189   |   7:    68.301 -  77.819:   19        |
|      3:    30.226 -  39.745:  137   |   8:    77.819 -  87.338:    4        |
|      4:    39.745 -  49.263:  115   |   9:    87.338 -  96.857:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 281         
Filter by distance & map next to the model:
   mapped sites are within: 0.398 - 4.481
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 277 from: 281
   mapped sites are within: 0.751 - 4.481

peak=    6.041 closest distance to " O   HOH Z 126 " =    1.961
peak=    5.896 closest distance to " NH2 ARG A  56 " =    2.100
peak=    5.781 closest distance to " O   HOH Z 144 " =    1.838
peak=    5.768 closest distance to " NE2 GLN A  11 " =    1.122
peak=    5.311 closest distance to " CB  SER A  63 " =    1.179
peak=    5.297 closest distance to " O   HOH Z 278 " =    1.183
peak=    5.257 closest distance to " CB  ARG A 275 " =    0.928
peak=    5.168 closest distance to " CG  PRO A  54 " =    1.133
peak=    5.018 closest distance to " O   HOH Z 193 " =    1.783
peak=    4.870 closest distance to " CB  GLN A 183 " =    1.251
peak=    4.813 closest distance to " O   HOH Z 232 " =    2.307
peak=    4.781 closest distance to " O   HOH Z 260 " =    1.219
peak=    4.761 closest distance to " CB  GLN A 223 " =    1.521
peak=    4.694 closest distance to " O   HOH Z 108 " =    1.343
peak=    4.656 closest distance to " O   HOH Z  78 " =    1.742
peak=    4.637 closest distance to " O   HOH Z 234 " =    3.634
peak=    4.608 closest distance to " CB  ASN A 148 " =    1.754
peak=    4.607 closest distance to " O   HOH Z 427 " =    2.701
peak=    4.586 closest distance to " C   PRO A 198 " =    1.488
peak=    4.503 closest distance to " CG  PRO A 213 " =    1.210
peak=    4.455 closest distance to " O   HOH Z 124 " =    1.356
peak=    4.439 closest distance to " O   HOH Z   6 " =    2.099
peak=    4.426 closest distance to " O   HOH Z 207 " =    1.780
peak=    4.416 closest distance to " CB  GLU A 152 " =    1.234
peak=    4.411 closest distance to " OD2 ASP A 286 " =    2.647
peak=    4.376 closest distance to " O   HOH Z 316 " =    2.909
peak=    4.357 closest distance to " O   HOH Z 203 " =    1.802
peak=    4.353 closest distance to " CB  SER A   3 " =    1.295
peak=    4.330 closest distance to " O   HOH Z 298 " =    1.890
peak=    4.326 closest distance to " O   HOH Z 368 " =    1.881
peak=    4.314 closest distance to " CB  TYR A 169 " =    0.866
peak=    4.311 closest distance to " O   HOH Z 236 " =    1.394
peak=    4.261 closest distance to " O   HOH Z 287 " =    1.942
peak=    4.258 closest distance to " NZ  LYS A 117 " =    3.158
peak=    4.240 closest distance to " OD1 ASN A  69 " =    2.606
peak=    4.239 closest distance to " O   HOH Z 213 " =    1.838
peak=    4.234 closest distance to " O   HOH Z  93 " =    2.144
peak=    4.192 closest distance to " O   HOH Z  54 " =    1.658
peak=    4.184 closest distance to " O   SER A  87 " =    2.299
peak=    4.179 closest distance to " CA  ALA A  21 " =    1.091
peak=    4.177 closest distance to " CA  TYR A  30 " =    0.990
peak=    4.158 closest distance to " O   HOH Z 272 " =    1.854
peak=    4.156 closest distance to " O   HOH Z  59 " =    1.941
peak=    4.155 closest distance to " O   HOH Z 209 " =    2.237
peak=    4.154 closest distance to " O   HOH Z 134 " =    1.326
peak=    4.151 closest distance to " CB  GLU A 128 " =    1.085
peak=    4.100 closest distance to " O   HOH Z  15 " =    2.242
peak=    4.088 closest distance to " O   HOH Z 369 " =    1.986
peak=    4.074 closest distance to " OG BSER A 164 " =    2.422
peak=    4.070 closest distance to " O   HOH Z 132 " =    0.998
peak=    4.053 closest distance to " O   HOH Z  78 " =    2.102
peak=    4.046 closest distance to " O   HOH Z  61 " =    1.613
peak=    4.036 closest distance to " CB  PRO A  54 " =    0.927
peak=    4.032 closest distance to " O   HOH Z 344 " =    2.944
peak=    4.021 closest distance to " CB  LEU A 228 " =    1.109
peak=    4.014 closest distance to " NH1BARG A 145 " =    1.414
peak=    3.993 closest distance to " CG  PRO A  90 " =    1.153
peak=    3.988 closest distance to " ND2 ASN A 187 " =    1.509
peak=    3.961 closest distance to " O   HOH Z 284 " =    2.808
peak=    3.954 closest distance to " O   HOH Z  43 " =    2.007
peak=    3.950 closest distance to " O   HOH Z  10 " =    1.812
peak=    3.946 closest distance to " CB  ARG A  79 " =    1.533
peak=    3.935 closest distance to " CG1 ILE A  33 " =    1.239
peak=    3.921 closest distance to " O   HOH Z 346 " =    1.658
peak=    3.919 closest distance to " O   HOH Z  97 " =    1.969
peak=    3.919 closest distance to " O   HOH Z 173 " =    1.921
peak=    3.908 closest distance to " O   MET A 105 " =    1.824
peak=    3.907 closest distance to " O   HOH Z 156 " =    3.040
peak=    3.899 closest distance to " O   HOH Z 128 " =    2.082
peak=    3.895 closest distance to " CB  VAL A 265 " =    1.377
peak=    3.879 closest distance to " O   HOH Z 144 " =    2.182
peak=    3.877 closest distance to " O   HOH Z   3 " =    1.843
peak=    3.871 closest distance to " O   HOH Z 234 " =    3.791
peak=    3.865 closest distance to " CA  THR A 221 " =    0.917
peak=    3.860 closest distance to " O   HOH Z 263 " =    2.223
peak=    3.855 closest distance to " O   HOH Z 380 " =    1.984
peak=    3.854 closest distance to " O   HOH Z 250 " =    1.307
peak=    3.845 closest distance to " CB  TRP A 179 " =    1.270
peak=    3.816 closest distance to " O   HOH Z 128 " =    2.021
peak=    3.815 closest distance to " O   HOH Z 389 " =    1.726
peak=    3.814 closest distance to " O   HOH Z 326 " =    1.469
peak=    3.804 closest distance to " O   HOH Z 407 " =    2.317
peak=    3.792 closest distance to " O   HOH Z 313 " =    1.659
peak=    3.785 closest distance to " O   HOH Z  73 " =    1.659
peak=    3.781 closest distance to " O   HOH Z  44 " =    1.948
peak=    3.777 closest distance to " O   HOH Z 193 " =    2.055
peak=    3.758 closest distance to " O   HOH Z 425 " =    1.291
peak=    3.754 closest distance to " CB  SER A  26 " =    1.561
peak=    3.747 closest distance to " O   HOH Z 411 " =    3.768
peak=    3.743 closest distance to " O   HOH Z 108 " =    2.000
peak=    3.740 closest distance to " O   HOH Z  40 " =    1.563
peak=    3.724 closest distance to " O   HOH Z 327 " =    1.690
peak=    3.723 closest distance to " CD2 TRP A 179 " =    1.393
peak=    3.718 closest distance to " CG  PRO A 198 " =    1.237
peak=    3.709 closest distance to " O   HOH Z 402 " =    1.394
peak=    3.707 closest distance to " O   HOH Z 403 " =    1.707
peak=    3.694 closest distance to " N   ASN A  39 " =    1.207
peak=    3.692 closest distance to " CG  ARG A  66 " =    2.719
peak=    3.692 closest distance to " O   HOH Z  88 " =    2.902
peak=    3.685 closest distance to " O   HOH Z 303 " =    2.038
peak=    3.681 closest distance to " CA  THR A 264 " =    0.841
peak=    3.679 closest distance to " CB  ARG A 139 " =    1.000
peak=    3.673 closest distance to " O   HOH Z  71 " =    1.456
peak=    3.673 closest distance to " O   HOH Z 172 " =    3.578
peak=    3.673 closest distance to " O   HOH Z 183 " =    1.571
peak=    3.670 closest distance to " O   HOH Z 392 " =    2.927
peak=    3.659 closest distance to " O   HOH Z 227 " =    1.767
peak=    3.657 closest distance to " O   HOH Z  21 " =    1.693
peak=    3.654 closest distance to " NH2BARG A 145 " =    2.017
peak=    3.653 closest distance to " O   HOH Z 426 " =    1.499
peak=    3.650 closest distance to " O   HOH Z 180 " =    2.233
peak=    3.647 closest distance to " O   HOH Z 423 " =    1.953
peak=    3.647 closest distance to " O   HOH Z   1 " =    1.780
peak=    3.646 closest distance to " O   HOH Z 366 " =    2.876
peak=    3.645 closest distance to " O   HOH Z 279 " =    2.122
peak=    3.641 closest distance to " CB  TRP A 266 " =    1.089
peak=    3.637 closest distance to " N   ARG A 156 " =    1.237
peak=    3.613 closest distance to " CG2 ILE A 120 " =    1.176
peak=    3.607 closest distance to " O   HOH Z 261 " =    1.881
peak=    3.599 closest distance to " CA  ASN A 176 " =    1.118
peak=    3.599 closest distance to " CG  GLN A  77 " =    2.161
peak=    3.598 closest distance to " CB  VAL A 202 " =    1.625
peak=    3.595 closest distance to " O   HOH Z 374 " =    2.427
peak=    3.594 closest distance to " CD BLYS A 290 " =    1.196
peak=    3.592 closest distance to " OG  SER A  22 " =    2.690
peak=    3.591 closest distance to " O   HOH Z 273 " =    2.865
peak=    3.588 closest distance to " O   HOH Z  48 " =    1.411
peak=    3.584 closest distance to " O   HOH Z  66 " =    2.084
peak=    3.580 closest distance to " O   HOH Z 425 " =    1.950
peak=    3.580 closest distance to " O   HOH Z 353 " =    2.543
peak=    3.572 closest distance to " CE2 TRP A 179 " =    1.560
peak=    3.568 closest distance to " CA  ASN A 215 " =    1.204
peak=    3.568 closest distance to " O   HOH Z 106 " =    2.104
peak=    3.565 closest distance to " O   HOH Z 106 " =    1.747
peak=    3.561 closest distance to " O   HOH Z  85 " =    1.634
peak=    3.558 closest distance to " CG  PRO A 243 " =    1.208
peak=    3.555 closest distance to " O   HOH Z 368 " =    3.657
peak=    3.553 closest distance to " CG AARG A 275 " =    0.978
peak=    3.540 closest distance to " O   HOH Z 286 " =    2.323
peak=    3.533 closest distance to " NH1AARG A 145 " =    1.051
peak=    3.528 closest distance to " O   HOH Z 261 " =    1.605
peak=    3.525 closest distance to " O   HOH Z 132 " =    2.194
peak=    3.524 closest distance to " O   HOH Z 281 " =    4.481
peak=    3.518 closest distance to " O   HOH Z 357 " =    1.766
peak=    3.514 closest distance to " CE1 TYR A 186 " =    1.217
peak=    3.510 closest distance to " O   HOH Z   9 " =    2.053
peak=    3.509 closest distance to " CG2 VAL A 257 " =    0.856
peak=    3.509 closest distance to " O   HOH Z  61 " =    1.602
peak=    3.507 closest distance to " O   HOH Z 291 " =    1.558
peak=    3.506 closest distance to " OG  SER A  62 " =    2.926
peak=    3.503 closest distance to " O   ALA A   1 " =    1.644
peak=    3.494 closest distance to " CB  SER A 141 " =    1.103
peak=    3.477 closest distance to " O   HOH Z 158 " =    2.957
peak=    3.476 closest distance to " O   HOH Z  63 " =    2.251
peak=    3.471 closest distance to " N   PHE A 130 " =    1.385
peak=    3.462 closest distance to " O   HOH Z  40 " =    1.907
peak=    3.460 closest distance to " CB  ARG A 190 " =    1.741
peak=    3.458 closest distance to " O   HOH Z  49 " =    2.017
peak=    3.456 closest distance to " O   HOH Z 125 " =    2.272
peak=    3.455 closest distance to " O   HOH Z 334 " =    1.333
peak=    3.451 closest distance to " CD2 LEU A 297 " =    0.976
peak=    3.450 closest distance to " O   HOH Z 214 " =    2.034
peak=    3.448 closest distance to " NE2 GLN A  58 " =    4.279
peak=    3.446 closest distance to " O   HOH Z 189 " =    1.553
peak=    3.439 closest distance to " CG1BVAL A  72 " =    1.377
peak=    3.436 closest distance to " O   HOH Z 112 " =    2.545
peak=    3.431 closest distance to " CG2 ILE A  20 " =    1.518
peak=    3.416 closest distance to " CA  MET A  40 " =    1.063
peak=    3.410 closest distance to " O   HOH Z 234 " =    1.847
peak=    3.408 closest distance to " CB  GLU A 277 " =    3.447
peak=    3.407 closest distance to " NH2 ARG A 219 " =    1.885
peak=    3.407 closest distance to " O   HOH Z 337 " =    3.627
peak=    3.399 closest distance to " O   HOH Z 227 " =    2.140
peak=    3.395 closest distance to " OD1 ASP A 231 " =    1.923
peak=    3.394 closest distance to " O   HOH Z 132 " =    2.355
peak=    3.391 closest distance to " O   SER A  26 " =    1.625
peak=    3.389 closest distance to " CG  GLU A 277 " =    2.127
peak=    3.387 closest distance to " O   HOH Z 192 " =    1.807
peak=    3.386 closest distance to " O   HOH Z 286 " =    2.171
peak=    3.382 closest distance to " O   HOH Z 219 " =    2.042
peak=    3.376 closest distance to " CA  VAL A  41 " =    0.898
peak=    3.374 closest distance to " CG  MET A 185 " =    1.078
peak=    3.368 closest distance to " CB  ASN A  39 " =    0.858
peak=    3.368 closest distance to " O   HOH Z 287 " =    2.112
peak=    3.367 closest distance to " O   HOH Z  59 " =    2.133
peak=    3.359 closest distance to " O   HOH Z 291 " =    1.824
peak=    3.354 closest distance to " CG2BVAL A  41 " =    0.901
peak=    3.350 closest distance to " OG BSER A 258 " =    3.392
peak=    3.334 closest distance to " O   HOH Z  19 " =    2.330
peak=    3.334 closest distance to " CA  ALA A 291 " =    0.929
peak=    3.330 closest distance to " CD2 LEU A 255 " =    1.393
peak=    3.327 closest distance to " CA  ALA A 233 " =    1.056
peak=    3.323 closest distance to " O   HOH Z 271 " =    2.012
peak=    3.323 closest distance to " O   HOH Z  64 " =    2.066
peak=    3.317 closest distance to " CG  MET A 185 " =    1.226
peak=    3.315 closest distance to " CG2 THR A 221 " =    1.120
peak=    3.310 closest distance to " CE AMET A  47 " =    1.213
peak=    3.299 closest distance to " CB  SER A  62 " =    1.366
peak=    3.298 closest distance to " O   HOH Z 345 " =    3.133
peak=    3.293 closest distance to " O   HOH Z 343 " =    1.261
peak=    3.291 closest distance to " O   HOH Z 194 " =    1.875
peak=    3.290 closest distance to " OE2 GLU A  53 " =    2.153
peak=    3.290 closest distance to " O   HOH Z 214 " =    0.916
peak=    3.289 closest distance to " O   HOH Z 211 " =    2.334
peak=    3.288 closest distance to " O   HOH Z 150 " =    1.798
peak=    3.286 closest distance to " O   HOH Z 287 " =    1.803
peak=    3.286 closest distance to " O   HOH Z 248 " =    1.797
peak=    3.285 closest distance to " O   HOH Z 427 " =    3.024
peak=    3.280 closest distance to " O   HOH Z  43 " =    2.685
peak=    3.279 closest distance to " O   HOH Z 392 " =    1.913
peak=    3.277 closest distance to " C   TYR A 214 " =    1.411
peak=    3.276 closest distance to " O   ALA A   1 " =    1.458
peak=    3.275 closest distance to " CB  GLN A  88 " =    1.199
peak=    3.272 closest distance to " NH2AARG A 190 " =    1.221
peak=    3.269 closest distance to " O   HOH Z 433 " =    1.768
peak=    3.258 closest distance to " CA  ASP A 140 " =    1.077
peak=    3.258 closest distance to " CE BMET A  47 " =    1.357
peak=    3.252 closest distance to " CD  LYS A 166 " =    1.268
peak=    3.251 closest distance to " O   HOH Z 334 " =    1.529
peak=    3.247 closest distance to " O   HOH Z 214 " =    2.345
peak=    3.245 closest distance to " CB  ALA A 291 " =    1.394
peak=    3.237 closest distance to " NZ  LYS A  76 " =    1.292
peak=    3.237 closest distance to " O   HOH Z 163 " =    1.776
peak=    3.232 closest distance to " O   HOH Z 151 " =    1.567
peak=    3.228 closest distance to " O   HOH Z 280 " =    1.703
peak=    3.227 closest distance to " O   HOH Z 411 " =    1.711
peak=    3.221 closest distance to " CB  ARG A 102 " =    0.784
peak=    3.220 closest distance to " O   HOH Z 422 " =    2.715
peak=    3.219 closest distance to " CB  ALA A  34 " =    1.031
peak=    3.213 closest distance to " OD1BASN A 224 " =    2.254
peak=    3.208 closest distance to " NH1 ARG A  14 " =    1.064
peak=    3.207 closest distance to " CA  ASN A 217 " =    1.241
peak=    3.205 closest distance to " CA  ALA A 248 " =    1.207
peak=    3.203 closest distance to " O   HOH Z  40 " =    2.672
peak=    3.202 closest distance to " O   HOH Z  30 " =    2.178
peak=    3.199 closest distance to " O   HOH Z 336 " =    1.694
peak=    3.197 closest distance to " O   HOH Z 388 " =    1.871
peak=    3.193 closest distance to " O   HOH Z 368 " =    2.607
peak=    3.192 closest distance to " O   ALA A 165 " =    1.341
peak=    3.188 closest distance to " CG  MET A 113 " =    1.101
peak=    3.184 closest distance to " O   HOH Z 135 " =    1.621
peak=    3.177 closest distance to " O   HOH Z 329 " =    3.429
peak=    3.169 closest distance to " CG  GLN A  89 " =    1.476
peak=    3.169 closest distance to " CA  PHE A 283 " =    1.395
peak=    3.168 closest distance to " O   HOH Z  85 " =    2.218
peak=    3.159 closest distance to " CA  GLY A  80 " =    0.796
peak=    3.157 closest distance to " O   HOH Z 409 " =    2.790
peak=    3.151 closest distance to " CB  THR A  31 " =    1.731
peak=    3.149 closest distance to " CG  MET A  93 " =    0.963
peak=    3.149 closest distance to " CA  LEU A 282 " =    1.231
peak=    3.137 closest distance to " N   ASN A 127 " =    1.219
peak=    3.134 closest distance to " O   HOH Z 148 " =    3.151
peak=    3.131 closest distance to " CB  ASN A 110 " =    1.086
peak=    3.122 closest distance to " CA  LEU A 300 " =    1.096
peak=    3.120 closest distance to " C   ALA A 299 " =    0.963
peak=    3.116 closest distance to " CA  ALA A  84 " =    1.374
peak=    3.112 closest distance to " O   HOH Z 266 " =    3.008
peak=    3.107 closest distance to " O   HOH Z 435 " =    1.889
peak=    3.106 closest distance to " CB  MET A  47 " =    1.173
peak=    3.106 closest distance to " O   HOH Z 379 " =    1.874
peak=    3.105 closest distance to " CD  PRO A 243 " =    1.566
peak=    3.100 closest distance to " O   HOH Z 255 " =    1.627
peak=    3.098 closest distance to " O   HOH Z 328 " =    2.044
peak=    3.094 closest distance to " O   HOH Z 245 " =    1.304
peak=    3.093 closest distance to " CG2 THR A 294 " =    1.565
peak=    3.087 closest distance to " CA  VAL A 126 " =    1.191
peak=    3.084 closest distance to " CB  SER A 216 " =    0.751
peak=    3.079 closest distance to " O   HOH Z 216 " =    2.331
peak=    3.076 closest distance to " O   HOH Z 188 " =    1.941
peak=    3.074 closest distance to " CB  TYR A  30 " =    1.458
peak=    3.070 closest distance to " ND1 HIS A  86 " =    1.874
peak=    3.064 closest distance to " O   HOH Z 251 " =    1.591
peak=    3.055 closest distance to " CA  ALA A 158 " =    1.111
peak=    3.055 closest distance to " CD2 HIS A  81 " =    1.132
peak=    3.052 closest distance to " O   HOH Z  68 " =    1.510
peak=    3.041 closest distance to " O   HOH Z 115 " =    1.847
peak=    3.027 closest distance to " O   HOH Z 346 " =    1.431

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 185         
Filter by distance & map next to the model:
   mapped sites are within: 0.766 - 5.906
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 185 from: 185
   mapped sites are within: 0.766 - 5.906

peak=   -4.514 closest distance to " O   HOH Z 266 " =    4.288
peak=   -4.424 closest distance to " N   GLN A  58 " =    1.653
peak=   -4.378 closest distance to " SG  CYS A 254 " =    3.257
peak=   -4.371 closest distance to " OXT GLY A 302 " =    2.670
peak=   -4.339 closest distance to " CD  ARG A 156 " =    1.993
peak=   -4.319 closest distance to " CB  TYR A  15 " =    2.216
peak=   -4.289 closest distance to " O   HOH Z 377 " =    2.093
peak=   -4.270 closest distance to " C   HIS A 108 " =    1.097
peak=   -4.257 closest distance to " O   HOH Z  13 " =    1.335
peak=   -4.202 closest distance to " O   VAL A  67 " =    2.683
peak=   -4.172 closest distance to " CB  PRO A 243 " =    2.542
peak=   -4.146 closest distance to " O   HOH Z 290 " =    1.029
peak=   -4.101 closest distance to " O   HOH Z 198 " =    2.010
peak=   -4.099 closest distance to " CG  LYS A 193 " =    2.263
peak=   -4.082 closest distance to " N   ALA A 248 " =    1.604
peak=   -4.031 closest distance to " O   HOH Z  52 " =    1.444
peak=   -4.000 closest distance to " O   PRO A 198 " =    1.304
peak=   -3.974 closest distance to " O   ILE A 109 " =    2.541
peak=   -3.966 closest distance to " CA  VAL A  67 " =    2.774
peak=   -3.939 closest distance to " O   VAL A 153 " =    2.325
peak=   -3.914 closest distance to " CB  ASN A  39 " =    2.152
peak=   -3.889 closest distance to " O   HOH Z 435 " =    2.672
peak=   -3.888 closest distance to " OG  SER A  97 " =    2.006
peak=   -3.885 closest distance to " C   ALA A 158 " =    1.190
peak=   -3.872 closest distance to " O   HOH Z 407 " =    3.001
peak=   -3.867 closest distance to " O   HOH Z 102 " =    1.758
peak=   -3.864 closest distance to " CZ  PHE A  59 " =    1.539
peak=   -3.848 closest distance to " O   HOH Z 385 " =    2.077
peak=   -3.830 closest distance to " O   HOH Z 388 " =    2.000
peak=   -3.828 closest distance to " O   HOH Z  43 " =    1.631
peak=   -3.815 closest distance to " CZ  TYR A 169 " =    1.749
peak=   -3.799 closest distance to " O   ALA A 161 " =    1.672
peak=   -3.788 closest distance to " CB  ALA A 291 " =    2.391
peak=   -3.788 closest distance to " CA  GLY A  98 " =    1.942
peak=   -3.783 closest distance to " CG  GLN A 223 " =    1.937
peak=   -3.776 closest distance to " OG BSER A 134 " =    1.214
peak=   -3.757 closest distance to " O   HOH Z 126 " =    1.855
peak=   -3.746 closest distance to " CE2 TYR A  30 " =    2.874
peak=   -3.730 closest distance to " O   HOH Z  24 " =    1.343
peak=   -3.729 closest distance to " N   HIS A 115 " =    1.806
peak=   -3.713 closest distance to " N   ASP A 286 " =    2.288
peak=   -3.712 closest distance to " O   HOH Z  93 " =    1.513
peak=   -3.711 closest distance to " O   HOH Z 263 " =    2.848
peak=   -3.711 closest distance to " CD2 LEU A 300 " =    2.872
peak=   -3.710 closest distance to " O   HOH Z 231 " =    2.016
peak=   -3.702 closest distance to " O   HOH Z  11 " =    1.921
peak=   -3.701 closest distance to " OXT GLY A 302 " =    3.454
peak=   -3.679 closest distance to " CD1 LEU A 101 " =    2.323
peak=   -3.677 closest distance to " O   HOH Z 198 " =    1.439
peak=   -3.676 closest distance to " CD  ARG A 139 " =    1.561
peak=   -3.675 closest distance to " O   HOH Z 185 " =    2.132
peak=   -3.673 closest distance to " ND2 ASN A  45 " =    0.944
peak=   -3.661 closest distance to " NH1 ARG A 195 " =    2.556
peak=   -3.660 closest distance to " CE3 TRP A 274 " =    2.335
peak=   -3.651 closest distance to " O   SER A 146 " =    0.910
peak=   -3.648 closest distance to " O   HOH Z   3 " =    1.772
peak=   -3.646 closest distance to " O   HOH Z 118 " =    2.827
peak=   -3.607 closest distance to " N   GLN A 122 " =    1.439
peak=   -3.606 closest distance to " CG  PHE A 283 " =    2.594
peak=   -3.591 closest distance to " CD1 PHE A  59 " =    1.852
peak=   -3.586 closest distance to " CG  ASP A 231 " =    0.766
peak=   -3.580 closest distance to " O   HOH Z 351 " =    1.540
peak=   -3.576 closest distance to " CZ3 TRP A 179 " =    1.332
peak=   -3.575 closest distance to " OH  TYR A 214 " =    1.277
peak=   -3.574 closest distance to " O   PRO A 163 " =    1.910
peak=   -3.574 closest distance to " O   HOH Z 362 " =    5.906
peak=   -3.572 closest distance to " O   HOH Z  11 " =    1.795
peak=   -3.564 closest distance to " O   SER A 135 " =    1.561
peak=   -3.563 closest distance to " CD1 LEU A 228 " =    2.109
peak=   -3.549 closest distance to " O   HOH Z  47 " =    1.526
peak=   -3.541 closest distance to " OG  SER A   3 " =    1.665
peak=   -3.541 closest distance to " O   MET A  40 " =    2.683
peak=   -3.540 closest distance to " O   HOH Z 353 " =    2.179
peak=   -3.534 closest distance to " O   HOH Z  63 " =    1.404
peak=   -3.534 closest distance to " O   HOH Z  88 " =    1.796
peak=   -3.531 closest distance to " CA  GLY A 133 " =    1.894
peak=   -3.529 closest distance to " O   HOH Z 166 " =    1.385
peak=   -3.526 closest distance to " O   HOH Z  88 " =    2.313
peak=   -3.517 closest distance to " N   SER A 276 " =    1.179
peak=   -3.512 closest distance to " CB  ALA A  43 " =    2.244
peak=   -3.509 closest distance to " O   HOH Z 395 " =    5.067
peak=   -3.492 closest distance to " O   HOH Z 250 " =    1.471
peak=   -3.482 closest distance to " NH2 ARG A  79 " =    1.898
peak=   -3.472 closest distance to " CE  MET A 105 " =    2.047
peak=   -3.472 closest distance to " CG1 VAL A 112 " =    2.835
peak=   -3.467 closest distance to " CB  ASP A 132 " =    2.285
peak=   -3.460 closest distance to " O   PRO A 198 " =    1.279
peak=   -3.460 closest distance to " CB  ALA A 248 " =    1.951
peak=   -3.458 closest distance to " O   SER A 210 " =    1.888
peak=   -3.455 closest distance to " O   VAL A 174 " =    1.957
peak=   -3.452 closest distance to " CA  GLY A 203 " =    2.273
peak=   -3.447 closest distance to " O   HOH Z  90 " =    2.648
peak=   -3.440 closest distance to " CD  GLU A 152 " =    2.582
peak=   -3.436 closest distance to " CB  CYS A 201 " =    2.464
peak=   -3.433 closest distance to " CB  ALA A  51 " =    1.870
peak=   -3.433 closest distance to " OD2 ASP A 171 " =    2.334
peak=   -3.429 closest distance to " O   ALA A  51 " =    1.248
peak=   -3.422 closest distance to " O   HOH Z 389 " =    1.809
peak=   -3.415 closest distance to " ND2 ASN A 187 " =    1.495
peak=   -3.405 closest distance to " NE2 GLN A  58 " =    1.230
peak=   -3.399 closest distance to " O   PHE A 218 " =    1.596
peak=   -3.394 closest distance to " C   LEU A 143 " =    1.104
peak=   -3.387 closest distance to " ND2 ASN A  45 " =    1.078
peak=   -3.387 closest distance to " N   THR A 157 " =    1.590
peak=   -3.377 closest distance to " O   HOH Z 436 " =    1.231
peak=   -3.375 closest distance to " O   HOH Z 385 " =    1.899
peak=   -3.374 closest distance to " CD1 ILE A 239 " =    2.480
peak=   -3.365 closest distance to " OD1 ASP A 191 " =    1.787
peak=   -3.353 closest distance to " N   GLN A  58 " =    1.288
peak=   -3.352 closest distance to " OG BSER A 134 " =    1.667
peak=   -3.349 closest distance to " O   HOH Z 165 " =    2.139
peak=   -3.338 closest distance to " O   HOH Z 298 " =    1.252
peak=   -3.338 closest distance to " CB  PRO A 163 " =    2.609
peak=   -3.333 closest distance to " CB  ALA A 244 " =    2.018
peak=   -3.329 closest distance to " OG ASER A 134 " =    1.030
peak=   -3.329 closest distance to " O   HOH Z  97 " =    1.549
peak=   -3.324 closest distance to " CB  ALA A 291 " =    2.229
peak=   -3.324 closest distance to " CB  ASP A 149 " =    2.028
peak=   -3.320 closest distance to " CG2 VAL A 189 " =    2.060
peak=   -3.320 closest distance to " CG  MET A 105 " =    0.943
peak=   -3.318 closest distance to " CA  ASP A 298 " =    1.037
peak=   -3.316 closest distance to " O   HOH Z 310 " =    3.410
peak=   -3.313 closest distance to " O   TRP A  70 " =    1.535
peak=   -3.309 closest distance to " CD2 LEU A 300 " =    2.774
peak=   -3.307 closest distance to " CB  PHE A 192 " =    1.786
peak=   -3.305 closest distance to " CG2AVAL A  41 " =    2.747
peak=   -3.300 closest distance to " C   TRP A 274 " =    1.554
peak=   -3.297 closest distance to " O   LYS A 117 " =    1.493
peak=   -3.267 closest distance to " CD2 LEU A 237 " =    2.461
peak=   -3.261 closest distance to " SG ACYS A 201 " =    2.004
peak=   -3.258 closest distance to " O   ASP A 231 " =    2.415
peak=   -3.255 closest distance to " OD1 ASP A 191 " =    1.362
peak=   -3.253 closest distance to " ND2 ASN A  39 " =    1.402
peak=   -3.251 closest distance to " NH2 ARG A  66 " =    4.441
peak=   -3.250 closest distance to " O   HOH Z  60 " =    1.902
peak=   -3.248 closest distance to " O   TRP A  92 " =    1.675
peak=   -3.247 closest distance to " N   ALA A  43 " =    2.248
peak=   -3.240 closest distance to " CG  GLU A 152 " =    1.128
peak=   -3.236 closest distance to " CB  PHE A 208 " =    2.200
peak=   -3.232 closest distance to " CA  TRP A  70 " =    2.498
peak=   -3.222 closest distance to " C   GLN A 205 " =    1.943
peak=   -3.216 closest distance to " O   HOH Z 427 " =    1.408
peak=   -3.215 closest distance to " OG BSER A 210 " =    1.767
peak=   -3.214 closest distance to " OD2 ASP A  50 " =    1.386
peak=   -3.198 closest distance to " OD1 ASP A 171 " =    1.613
peak=   -3.197 closest distance to " CA  TYR A  30 " =    2.868
peak=   -3.193 closest distance to " OD2 ASP A 270 " =    1.287
peak=   -3.186 closest distance to " CE3 TRP A 123 " =    1.251
peak=   -3.184 closest distance to " O   HOH Z 361 " =    3.427
peak=   -3.183 closest distance to " O   ALA A 292 " =    1.932
peak=   -3.178 closest distance to " CG  PRO A 243 " =    1.559
peak=   -3.171 closest distance to " ND2 ASN A 209 " =    1.710
peak=   -3.166 closest distance to " O   HOH Z 148 " =    1.801
peak=   -3.165 closest distance to " CG  ARG A 219 " =    2.522
peak=   -3.157 closest distance to " CE2 PHE A 218 " =    2.488
peak=   -3.154 closest distance to " O   HOH Z 281 " =    2.888
peak=   -3.153 closest distance to " CG1 VAL A 112 " =    2.894
peak=   -3.152 closest distance to " CD2 TYR A 293 " =    2.031
peak=   -3.142 closest distance to " CD1 ILE A 239 " =    2.054
peak=   -3.141 closest distance to " CD  GLN A  88 " =    0.927
peak=   -3.137 closest distance to " O   HOH Z 210 " =    1.160
peak=   -3.137 closest distance to " O   SER A  22 " =    2.352
peak=   -3.132 closest distance to " CB  ALA A 100 " =    2.568
peak=   -3.126 closest distance to " OE1 GLN A  88 " =    1.315
peak=   -3.126 closest distance to " O   VAL A 189 " =    2.500
peak=   -3.111 closest distance to " CE2 PHE A 192 " =    2.010
peak=   -3.109 closest distance to " ND2 ASN A  69 " =    1.377
peak=   -3.109 closest distance to " O   HOH Z 234 " =    4.007
peak=   -3.107 closest distance to " CG  PRO A 163 " =    2.603
peak=   -3.104 closest distance to " CA  ASP A  27 " =    2.317
peak=   -3.092 closest distance to " CE  MET A  93 " =    1.173
peak=   -3.091 closest distance to " CG2 ILE A 263 " =    2.163
peak=   -3.087 closest distance to " O   HOH Z 396 " =    1.599
peak=   -3.084 closest distance to " OE2 GLU A 152 " =    1.255
peak=   -3.078 closest distance to " O   HOH Z 389 " =    4.482
peak=   -3.076 closest distance to " O   HOH Z 378 " =    1.736
peak=   -3.075 closest distance to " O   HOH Z 137 " =    1.469
peak=   -3.067 closest distance to " OG  SER A 206 " =    1.630
peak=   -3.064 closest distance to " O   HOH Z 298 " =    2.422
peak=   -3.059 closest distance to " OD1 ASP A 200 " =    1.273
peak=   -3.057 closest distance to " CG1AVAL A  41 " =    2.755
peak=   -3.051 closest distance to " O   SER A 146 " =    0.937
peak=   -3.050 closest distance to " CE  MET A 105 " =    1.969
peak=   -3.018 closest distance to " OD1 ASN A 249 " =    1.152
peak=   -3.018 closest distance to " O   HOH Z  15 " =    1.790

================= 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    :  0.3998 0.3994   6.192830e+00   6.194982e+00
   1_bss:  0.3861 0.3816   6.180470e+00   6.164925e+00
   1_xyz:  0.2760 0.2995   5.909436e+00   5.978344e+00
   1_adp:  0.2527 0.3068   5.855152e+00   5.994653e+00
   1_occ:  0.2525 0.3070   5.854489e+00   5.994540e+00
   2_bss:  0.2497 0.3053   5.848330e+00   5.990570e+00
   2_xyz:  0.1854 0.2372   5.583795e+00   5.764169e+00
   2_adp:  0.1742 0.2215   5.522714e+00   5.705010e+00
   2_occ:  0.1736 0.2215   5.521703e+00   5.704730e+00
   3_bss:  0.1730 0.2205   5.516192e+00   5.697603e+00
   3_xyz:  0.1379 0.1791   5.307083e+00   5.510297e+00
   3_adp:  0.1285 0.1729   5.254412e+00   5.470626e+00
   3_occ:  0.1284 0.1728   5.253897e+00   5.470076e+00
   4_bss:  0.1287 0.1728   5.253293e+00   5.469913e+00
   4_xyz:  0.1163 0.1609   5.166767e+00   5.394261e+00
   4_adp:  0.1140 0.1589   5.151220e+00   5.379968e+00
   4_occ:  0.1139 0.1587   5.150610e+00   5.379361e+00
   5_bss:  0.1139 0.1587   5.150583e+00   5.379417e+00
   5_xyz:  0.1074 0.1554   5.114459e+00   5.363352e+00
   5_adp:  0.1067 0.1549   5.109640e+00   5.359885e+00
   5_occ:  0.1067 0.1548   5.109433e+00   5.359850e+00
   5_bss:  0.1066 0.1548   5.109509e+00   5.359924e+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:  0.322  20.000  -2.351  -2.283   3.412  -0.000   0.000   0.000
   1_xyz:  0.322  20.000  -2.351  -2.283   3.412  -0.000   0.000   0.000
   1_adp:  0.322  20.000  -2.351  -2.283   3.412  -0.000   0.000   0.000
   1_occ:  0.322  20.000  -2.351  -2.283   3.412  -0.000   0.000   0.000
   2_bss:  0.322  33.468  -2.545  -2.063   0.611  -0.000   0.000   0.000
   2_xyz:  0.322  33.468  -2.545  -2.063   0.611  -0.000   0.000   0.000
   2_adp:  0.322  33.468  -2.545  -2.063   0.611  -0.000   0.000   0.000
   2_occ:  0.322  33.468  -2.545  -2.063   0.611  -0.000   0.000   0.000
   3_bss:  0.322  33.468  -2.798  -2.456  -1.140  -0.000  -0.000  -0.000
   3_xyz:  0.322  33.468  -2.798  -2.456  -1.140  -0.000  -0.000  -0.000
   3_adp:  0.322  33.468  -2.798  -2.456  -1.140  -0.000  -0.000  -0.000
   3_occ:  0.322  33.468  -2.798  -2.456  -1.140  -0.000  -0.000  -0.000
   4_bss:  0.315  36.595  -2.916  -2.544  -1.814  -0.000  -0.000  -0.000
   4_xyz:  0.315  36.595  -2.916  -2.544  -1.814  -0.000  -0.000  -0.000
   4_adp:  0.315  36.595  -2.916  -2.544  -1.814  -0.000  -0.000  -0.000
   4_occ:  0.315  36.595  -2.916  -2.544  -1.814  -0.000  -0.000  -0.000
   5_bss:  0.316  36.595  -2.796  -2.390  -1.874  -0.000  -0.000  -0.000
   5_xyz:  0.316  36.595  -2.796  -2.390  -1.874  -0.000  -0.000  -0.000
   5_adp:  0.316  36.595  -2.796  -2.390  -1.874  -0.000  -0.000  -0.000
   5_occ:  0.316  36.595  -2.796  -2.390  -1.874  -0.000  -0.000  -0.000
   5_bss:  0.321  37.577  -2.624  -2.215  -1.747  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  45.379 0.5797  0.7761    50418.721
   1_bss:  43.579 0.5997  0.7912    45325.192
   1_xyz:  31.161 0.7453  0.9436    24599.472
   1_adp:  32.430 0.7300  0.9335    25799.720
   1_occ:  32.433 0.7300  0.9334    25789.971
   2_bss:  32.022 0.7345  0.9105    25335.999
   2_xyz:  23.651 0.8249  0.9898    14595.502
   2_adp:  21.478 0.8477  1.0045    12694.920
   2_occ:  21.470 0.8478  1.0041    12685.004
   3_bss:  21.188 0.8503  0.9763    12380.143
   3_xyz:  16.638 0.8926  0.9984     8103.442
   3_adp:  15.785 0.9001  0.9968     7548.194
   3_occ:  15.767 0.9003  0.9968     7537.869
   4_bss:  15.734 0.9006  0.9866     7534.541
   4_xyz:  14.308 0.9121  0.9912     6412.346
   4_adp:  13.964 0.9152  0.9878     6265.013
   4_occ:  13.945 0.9153  0.9877     6254.014
   5_bss:  13.946 0.9153  0.9903     6257.614
   5_xyz:  13.581 0.9182  0.9916     5994.224
   5_adp:  13.466 0.9192  0.9880     5944.500
   5_occ:  13.461 0.9192  0.9878     5941.656
   5_bss:  13.462 0.9192  0.9914     5946.318
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.109   1.8721e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.109   1.8721e-01
   1_xyz:   1.233  0.010  0.076 15.451  0.006  4.106   9.0109e-02
   1_adp:   1.233  0.010  0.076 15.451  0.006  4.106   9.0109e-02
   1_occ:   1.233  0.010  0.076 15.451  0.006  4.106   9.0109e-02
   2_bss:   1.233  0.010  0.076 15.451  0.006  4.106   9.0109e-02
   2_xyz:   1.115  0.006  0.072 14.092  0.004  4.109   6.2358e-02
   2_adp:   1.115  0.006  0.072 14.092  0.004  4.109   6.2358e-02
   2_occ:   1.115  0.006  0.072 14.092  0.004  4.109   6.2358e-02
   3_bss:   1.115  0.006  0.072 14.092  0.004  4.109   6.2358e-02
   3_xyz:   0.896  0.005  0.063 14.117  0.004  4.107   4.8476e-02
   3_adp:   0.896  0.005  0.063 14.117  0.004  4.107   4.8476e-02
   3_occ:   0.896  0.005  0.063 14.117  0.004  4.107   4.8476e-02
   4_bss:   0.896  0.005  0.063 14.117  0.004  4.107   4.8476e-02
   4_xyz:   0.948  0.005  0.067 14.345  0.004  4.107   5.1924e-02
   4_adp:   0.948  0.005  0.067 14.345  0.004  4.107   5.1924e-02
   4_occ:   0.948  0.005  0.067 14.345  0.004  4.107   5.1924e-02
   5_bss:   0.948  0.005  0.067 14.345  0.004  4.107   5.1924e-02
   5_xyz:   1.043  0.007  0.073 14.695  0.004  4.107   6.2270e-02
   5_adp:   1.043  0.007  0.073 14.695  0.004  4.107   6.2270e-02
   5_occ:   1.043  0.007  0.073 14.695  0.004  4.107   6.2270e-02
   5_bss:   1.043  0.007  0.073 14.695  0.004  4.107   6.2270e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.429   2.3812e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.429   2.3812e-01
   1_xyz:   8.935  0.050  0.349 85.498  0.054  2.094   8.7165e-02
   1_adp:   8.935  0.050  0.349 85.498  0.054  2.094   8.7165e-02
   1_occ:   8.935  0.050  0.349 85.498  0.054  2.094   8.7165e-02
   2_bss:   8.935  0.050  0.349 85.498  0.054  2.094   8.7165e-02
   2_xyz:   7.057  0.035  0.242 81.884  0.039  2.357   5.4993e-02
   2_adp:   7.057  0.035  0.242 81.884  0.039  2.357   5.4993e-02
   2_occ:   7.057  0.035  0.242 81.884  0.039  2.357   5.4993e-02
   3_bss:   7.057  0.035  0.242 81.884  0.039  2.357   5.4993e-02
   3_xyz:   6.452  0.033  0.264 82.270  0.033  2.384   3.8216e-02
   3_adp:   6.452  0.033  0.264 82.270  0.033  2.384   3.8216e-02
   3_occ:   6.452  0.033  0.264 82.270  0.033  2.384   3.8216e-02
   4_bss:   6.452  0.033  0.264 82.270  0.033  2.384   3.8216e-02
   4_xyz:   6.096  0.045  0.203 84.143  0.034  2.315   3.2167e-02
   4_adp:   6.096  0.045  0.203 84.143  0.034  2.315   3.2167e-02
   4_occ:   6.096  0.045  0.203 84.143  0.034  2.315   3.2167e-02
   5_bss:   6.096  0.045  0.203 84.143  0.034  2.315   3.2167e-02
   5_xyz:   6.442  0.045  0.238 82.891  0.039  2.253   6.2237e-02
   5_adp:   6.442  0.045  0.238 82.891  0.039  2.253   6.2237e-02
   5_occ:   6.442  0.045  0.238 82.891  0.039  2.253   6.2237e-02
   5_bss:   6.442  0.045  0.238 82.891  0.039  2.253   6.2237e-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:  83.45   0.00  18.11  83.45   0.00  14.18  79.60   2.35  39.50
   1_occ:  83.45   0.00  18.11  83.45   0.00  14.18  79.60   2.35  39.50
   2_bss:  83.45   0.00  18.11  83.45   0.00  14.18  79.60   2.35  39.50
   2_xyz:  83.45   0.00  18.11  83.45   0.00  14.18  79.60   2.35  39.50
   2_adp:  83.05   0.92  17.40  83.05   0.92  13.57  74.50   6.52  38.24
   2_occ:  83.05   0.92  17.40  83.05   0.92  13.57  74.50   6.52  38.24
   3_bss:  83.05   0.92  17.40  83.05   0.92  13.57  74.50   6.52  38.24
   3_xyz:  83.05   0.92  17.40  83.05   0.92  13.57  74.50   6.52  38.24
   3_adp:  92.65   0.00  17.82  92.65   0.00  13.38  81.57   6.61  41.99
   3_occ:  92.65   0.00  17.82  92.65   0.00  13.38  81.57   6.61  41.99
   4_bss:  92.65   0.00  17.82  92.65   0.00  13.38  81.57   6.61  41.99
   4_xyz:  92.65   0.00  17.82  92.65   0.00  13.38  81.57   6.61  41.99
   4_adp:  94.89   1.60  17.50  94.89   1.60  13.18  83.95   6.39  41.04
   4_occ:  94.89   1.60  17.50  94.89   1.60  13.18  83.95   6.39  41.04
   5_bss:  94.89   1.60  17.50  94.89   1.60  13.18  83.95   6.39  41.04
   5_xyz:  94.89   1.60  17.50  94.89   1.60  13.18  83.95   6.39  41.04
   5_adp:  96.92   1.73  17.20  96.92   1.73  13.00  82.88   6.08  40.07
   5_occ:  96.92   1.73  17.20  96.92   1.73  13.00  82.88   6.08  40.07
   5_bss:  96.86   1.67  17.14  96.86   1.67  12.94  82.82   6.02  40.01
------------------------------------------------------------------------
 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:    1.783    0.009    0.298
   1_adp:    1.783    0.009    0.298
   1_occ:    1.783    0.009    0.298
   2_bss:    1.783    0.009    0.298
   2_xyz:    1.317    0.029    0.426
   2_adp:    1.317    0.029    0.426
   2_occ:    1.317    0.029    0.426
   3_bss:    1.317    0.029    0.426
   3_xyz:    1.332    0.026    0.505
   3_adp:    1.332    0.026    0.505
   3_occ:    1.332    0.026    0.505
   4_bss:    1.332    0.026    0.505
   4_xyz:    1.430    0.037    0.532
   4_adp:    1.430    0.037    0.532
   4_occ:    1.430    0.037    0.532
   5_bss:    1.430    0.037    0.532
   5_xyz:    1.364    0.057    0.552
   5_adp:    1.364    0.057    0.552
   5_occ:    1.364    0.057    0.552
   5_bss:    1.364    0.057    0.552
------------------------------------------------------------------------

CPU time actual refinement: 320.76


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_407/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_407/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_407/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_407/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_407/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 320.61 
  Macro-tasks:
    bulk solvent and scale       = 43.16  
    individual site refinement   = 128.91 
    weights calculation          = 28.48  
    collect and process          = 6.46   
    model show statistics        = 0.08   
    TOTAL for macro-tasks        = 207.09 
  Micro-tasks:
    mask                            = 1.74   
    f_calc                          = 99.78  
    alpha_beta                      = 7.91   
    target                          = 1.11   
    gradients_wrt_atomic_parameters = 108.02 
    fmodel                         = 6.77   
    r_factors                      = 0.22   
    phase_errors                   = 10.92  
    foms                           = 0.30   
    TOTAL for micro-tasks          = 236.77 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.579 micro seconds
Total CPU time: 5.57 minutes
from_scatterers_fft:    629 calls, 99.53 s
gradients_fft:          574 calls, 94.83 s

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

# Date 2008-01-16 Time 04:44:36 PST -0800 (1200487476.39 s)
Start R-work = 0.3998, R-free = 0.3994 (no bulk solvent and anisotropic scale)
Final R-work = 0.1333, R-free = 0.1767 (no bulk solvent and anisotropic scale)

Start R-work = 0.3861, R-free = 0.3816
Final R-work = 0.1066, R-free = 0.1548